Internal & external parasites in reptiles: 7 Signs You're Missing & Treatment Guide

You probably bought your reptile thinking you were getting a low-maintenance pet, ignoring the fact that you’re actually bringing a miniature ecosystem into your living room, one that often includes uninvited guests. The truth about Internal & external parasites in reptiles is that most keepers are completely oblivious to them until their animal is dangerously emaciated or the enclosure is crawling with visible pests.

After years of rehabbing rescues that arrived looking like deflated balloons, I can tell you that ignoring this reality is the fastest way to turn a $300 setup into a glass coffin.

Parasites aren't just an annoyance; they are a biological tax on your animal’s resources, stealing nutrients and causing stress that shuts down immune systems. Whether it’s a wild-caught import loaded with nematodes or a captive-bred gecko that picked up mites at a shady expo, the infestation is usually well underway before you spot the first symptom.

In my time managing shelter intakes, I’ve learned that "clean" animals are a myth and that proactive paranoia is the only strategy that works. Here is what decades of scrubbing tanks, dosing medications, and dealing with microscopic freeloaders has taught me about keeping your reptile from being eaten alive from the inside out.

Understanding Parasites: Why Most People Get It Wrong

There is a pervasive delusion in the hobby that if you buy a "captive bred" animal, you’re safe. That’s absolute garbage. While wild-caught animals are indeed biological ticking time bombs, captive collections are often breeding grounds for mites and protozoa due to poor quarantine practices and overcrowding.

The "Wild Caught" vs. "Captive Bred" Reality

Sellers love to slap "CB" (Captive Bred) on a deli cup and charge you a premium, implying the animal is sterile and healthy. Here’s the reality I’ve seen on the intake tables:

• The Expo Vector: Even healthy animals pick up mites (external) or cryptosporidium (internal) just by being on the same table as an infected animal at a show.
• The Stress Factor: Parasites often live in balance with a host in the wild. When you shove that animal into a glass box, transport it across the country, and mess up the humidity, the stress crashes their immune system, and the parasites take over.
• The Invisible Load: Most reptiles carry a low load of commensal organisms. It becomes "parasitic" only when the population explodes because the animal is stressed.

The Types of Freeloaders

You’re fighting a war on two fronts. External parasites are the ones you see; internal parasites are the ones that kill your pet while you wonder why they’re losing weight.

• External (Ectoparasites): Primarily mites and ticks. Mites look like moving dust (red, black, or grey). They suck blood, transmit diseases, and drive reptiles insane with itching.
• Internal (Endoparasites): This includes worms (nematodes, tapeworms, pinworms) and protozoa (coccidia, giardia, cryptosporidium). These destroy the gut lining, cause dehydration, and prevent nutrient absorption.

If you think you can spot internal parasites just by looking at the poop, you’re guessing. I’ve seen perfectly solid stools come from a dragon loaded with coccidia. You need a microscope, not intuition.

7 Signs You're Missing: The Parasite Checklist

Most keepers wait until their animal looks like a skeleton before realizing something is wrong. By then, the damage is severe. Here are the 7 definitive signs I look for during intake, if you see these, you’re already behind the curve.

1. Sign #1 - The "Healthy Eater" Weight Loss: This is the classic sign of internal worms. Your reptile is eating like a champion, maybe even more than usual, but the tail is getting thinner and the ribs are showing. The parasites are stealing the calories before the animal can absorb them. If you aren't weighing your reptile monthly on a gram scale ($15 on Amazon), you are flying blind. Sudden weight drops of 10% or more without a hunger strike are a massive red flag.
2. Sign #2 - The Water Bowl Soak: If a terrestrial reptile that usually hates water (like a Bearded Dragon or Ball Python) starts soaking in their water bowl for hours or days at a time, it’s not because they are having a spa day. They are trying to drown the mites crawling on their skin. Mites hate water, so the animal submerges to get relief from the biting. If you see this, check the water for tiny black specks floating on the surface, those are drowned mites.
3. Sign #3 - The "Rubbing" Behavior: A reptile with external parasites feels like you would if you were covered in mosquitoes. They will be restless, rubbing their heads or bodies against rough decor, rocks, or the glass sides of the enclosure. This isn't shedding behavior (which usually looks more systematic); this is frantic irritation. They are trying to mechanically scrape the bugs off their scales.
4. Sign #4 - The Unexplained Hiding (Lethargy): Reptiles hide when they feel vulnerable. Being sick makes them feel like prey. If your usually social Blue Tongue Skink or curious Gecko suddenly spends two weeks in the cool hide refusing to come out, they feel like trash. Parasites cause anemia (blood loss) and systemic malaise. A lethargic reptile is often an anemic reptile, drained of energy by blood-suckers or gut-destroyers.
5. Sign #5 - Abnormal Stool Consistency/Smell: Reptile poop smells bad, but parasite poop smells like something died and rotted in the sun. We’re talking room-clearing stench. Beyond the smell, look for consistency changes: diarrhea, mucus-coating, or blood are bad signs. Sometimes, in severe nematode infestations, you will actually see adult worms in the stool. If you see that, the infestation is massive.
6. Sign #6 - Raised Scales and "Dust": Look closely at your reptile’s eyes, armpits (axillary areas), and the vent. These are the soft spots where mites congregate. You might see raised scales because mites are wedged underneath them. You might see what looks like poppy seeds or ash moving around. If you crush one of these specks and it leaves a smear of red blood, congratulations, you have mites.
7. Sign #7 - Regurgitation: This is a severe sign. If your snake or lizard eats a meal and then throws it back up 2-3 days later, partially digested, their body is rejecting the effort of digestion. While this can be caused by low temperatures, in a heated tank, it’s often a sign of Crypto (Cryptosporidiosis) or a heavy worm load blocking the intestines. This is an emergency; regurgitation dehydrates a reptile incredibly fast.

Solutions: The Treatment Protocol That Works

Disclaimer: I am an experienced keeper, not a veterinarian. The advice below is for managing external parasites and supporting recovery. Internal parasites (worms/protozoa) require prescription medication (Panacur, Ponazuril, etc.) that you must get from a vet based on a fecal test. Do not guess with over-the-counter dewormers; you will kill your animal.

For external parasites (mites), you can treat this at home, but it is a war, not a battle. You must treat the animal AND the environment simultaneously.

Step 1: The Triage and Setup

If you find mites, your bioactive enclosure is dead. Accept it. You cannot save the isopods and springtails while killing the mites. You need to strip the tank completely.

1. Remove the Animal: Place them in a simple plastic tub with paper towels. This is their home for the next 6 weeks.
2. Strip the Tank: Throw away all substrate. Wood and porous rocks must be either boiled for 30 minutes or baked in the oven at 250°F for 2-3 hours. If it’s plastic, bleach it. If you can’t bake it or bleach it, trash it.
3. Cost Reality: You’re going to lose about $50-100 in substrate and decor. Don't try to save $20 of bark and reinfect your $400 animal.

Step 2: Treating the Animal (External Mites)

You need to kill the mites on the reptile without poisoning the reptile. This is a delicate balance.

For immediate relief, you need a spray that is safe for direct application. I’ve had consistent success using Natural Chemistry Reptile Relief Spray ↗ because unlike harsh chemicals, it uses natural oils to soften the waxy exoskeleton of the mite on contact, effectively dehydrating them without harming the reptile's skin.

If you are dealing with smaller reptiles or sensitive species where you are worried about sprays, you can try alternative formulations. Many keepers swear by Zoo Med Mite Off ↗ as a gentler alternative, which utilizes colloids to suffocate the parasites, making it a decent choice for animals that are already stressed and fragile.

For a more aggressive approach in the environment or on larger, hardier reptiles, JurassiPet JurassiMite ↗ offers a potent formula that targets mites, lice, and ticks, and I’ve found it useful for knocking down heavy infestations quickly.

The Procedure:
Apply the spray (avoiding eyes and nose), let it sit for a few minutes, then wipe the animal down. You will see dead mites coming off on the cloth. Repeat this every 3 days for 2-3 weeks to catch new hatchlings.

Step 3: Treating the Enclosure

While the animal is in the quarantine tub, you need to nuke the main tank. Mites lay eggs in the silicone corners and under the plastic rim.

You need a cleaner that cuts through organic waste where eggs hide. I typically saturate the empty tank with Exo Terra Terrarium Cleaner ↗, which is formulated to break down biological matter and stubborn residues, ensuring that there is no biofilm left for parasite eggs to adhere to.

Scrub the corners with a toothbrush. Rinse. Repeat. Let it dry completely. A dry tank kills mite eggs better than a damp one.

Step 4: Managing Internal Parasites (The Vet Visit)

For worms and protozoa, you need a "Fecal Float and Smear."
Cost: $40-80 at an exotic vet.
Process: Put a fresh poop sample in a Ziploc bag. Keep it in the fridge (not freezer) if you can’t go immediately. The vet looks under a microscope, identifies the specific egg, and gives you the specific poison to kill it.

Supportive Care:
Parasites drain fluids. A dehydrated reptile cannot metabolize medication. To help them bounce back, I always add a supplement to their soaking water. Using Zoo Med Reptile Electrolyte Soak ↗ during their warm baths provides essential B vitamins and electrolytes that help restore the fluid balance they’ve lost to diarrhea or blood-sucking mites.

Prevention: Building Your Fortress

If you think prevention is expensive, try paying a $400 emergency vet bill for a lizard that costs $50. Prevention is mostly about discipline, not money.

The Quarantine Protocol (The Rule Everyone Breaks)

Every new reptile, regardless of source, goes into quarantine. No exceptions.
The Setup: Plastic tub, paper towel substrate, plastic hide, water bowl.
The Timeline: Minimum 60 days. 90 is better.
The Logic: Mites have a lifecycle. You might not see them for 30 days. Internal parasites might not shed eggs in every stool. You need time to observe.

Hygiene Discipline

Cross-contamination is how you kill your whole collection.
Tools: Don’t use the same feeding tongs for your new gecko and your established boa.
Hands: Wash your hands between animals. Hand sanitizer is your best friend.
Substrate: Spot clean daily. Deep clean monthly. If it smells, you waited too long.

Common Mistakes: Why Most Fail

I’ve seen people battle mites for six months because they keep making the same rookie errors. Here is how to avoid the frustration loop.

Mistake #1: The "Olive Oil" Remedy

Internet forums love to suggest coating your snake in olive oil or vegetable oil to suffocate mites.
Why it fails: It makes a mess, it damages the scales if left on too long, and it doesn't kill the eggs in the tank. You end up with a greasy, miserable snake that still has mites two weeks later. Use actual parasiticides.

Mistake #2: Stopping Too Early

You treat the animal once, the mites disappear, and you put them back in the display tank.
Why it fails: Mite eggs take days or weeks to hatch. You killed the adults, but the next generation is waiting in the woodwork. You must continue treatment for at least one full lifecycle (usually 3-4 weeks) after the last visible mite is gone.

Mistake #3: Ignoring the Environment

Treating the animal but not the cage is like showering and putting your dirty clothes back on. The environment is 90% of the infestation. If you don't treat the surrounding area, including the carpet outside the tank, you will get re-infested.

Mistake #4: Using Mammal Products

Do not use dog or cat flea collars, sprays, or spot-ons unless explicitly directed by a specialized vet. Pyrethrins and permethrins can be neurotoxic to reptiles at the wrong dosage. I’ve seen snakes seizing and dying because their owner used a cut-up flea collar in the tank.

Perfect reptile keeping doesn't exist, I've failed enough times to know that. Even the best zoos get mites occasionally. The difference between a minor nuisance and a dead animal is how fast you react.

But armed with realistic expectations and these strategies, you can avoid the worst mistakes. Don't wait for the animal to look sick; assume they have parasites until proven otherwise.

Start by buying a gram scale and checking your animal's weight today. It's not glamorous, but it’s the single most useful tool you have to catch problems before they become tragedies.

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