Pseudoloma neurophilia (Microsporidia) is the most common pathogen detected in zebrafish (Danio rerio) from research facilities. The parasite infects the central nervous system and muscle and may be associated with emaciation and skeletal deformities. However, many fish exhibit subclinical infections. Another microsporidium, Pleistophora hyphessobryconis, has recently been detected in a few zebrafish facilities. Here, we review the methods for diagnosis and detection, modes of transmission, and approaches used to control microsporidia in zebrafish, focusing on P. neurophilia. The parasite can be readily transmitted by feeding spores or infected tissues, and we show that cohabitation with infected fish is also an effective means of transmission. Spores are released from live fish in various manners, including through the urine, feces, and sex products during spawning. Indeed, P. neurophilia infects both the eggs and ovarian tissues, where we found concentrations ranging from 12,000 to 88,000 spores per ovary. Hence, various lines of evidence support the conclusion that maternal transmission is a route of infection: spores are numerous in ovaries and developing follicles in infected females, spores are present in spawned eggs and water from spawning tanks based on polymerase chain reaction tests, and larvae are very susceptible to the infection. Furthermore, egg surface disinfectants presently used in zebrafish laboratories are ineffective against microsporidian spores. At this time, the most effective method for prevention of these parasites is avoidance.