Our zebrafish colony experienced a period of increased mortality rate of 6.5 times more deaths per month in a colony of over 13,000 zebrafish (Danio rerio), which developed over 3 months. We observed that before death, affected fish appeared emaciated, often with an abdominal bulge. We performed dissection on 18 fish that had this appearance and found in 15 that their gut was infected with a nematode that closely resembled Pseudocapillaria tomentosa. We devised a treatment protocol for this nematode infection, which involved addition of fenbendazole, a drug used to treat nematode infections in cattle and sheep, to the fish feed. Fenbendazole produced no severe side effects in the fish and several treatments have effectively eradicated the parasite from our colony. The mortality rate of our fish has decreased to a value of 0.7%/month (p<0.001, equal to that before the infection). We propose this protocol as an inexpensive alternative to having to rederive an entire colony from bleached eggs, and as a prophylactic measure used in quarantine facilities on a regular basis.