- Abstract Cryptocaryon irritans , a marine protozoan fish parasite with a life cycle that includes cyst formation, constitutes a major concern in intensive recirculating aquaculture systems (RASs), due to its potential propagation in a system with high fish density and minimal water change. In this study, the survival of C . irritans in sludge collected from an up-flow anaerobic sludge blanket (UASB) reactor of a RAS system was studied using a PCR assay. The detection sensitivity of the different life stages in sludge was determined to be 50 tomonts, 5 theronts and 5 trophonts. Dead C . irritans DNA was not detectable after 24 h of inoculation. The survival of the different C . irritans life stages in anaerobic conditions, as present in the UASB reactor, was evaluated. Theronts died within 3 h post-exposure to anaerobic conditions. Protomonts encysted within a day post-exposure, but unlike in aerobic conditions, the resulting tomonts did not hatch. Excystment of theronts from tomonts was delayed in anaerobic conditions, and occurred only after transfer to an aerobic environment. However, the tomonts did not die after 96 h of such exposure and the release rate of theronts did not decrease, compared to the control. The results suggest that infective theronts cannot originate from the UASB reactor and protomonts or theronts that reach the UASB do not survive. However, tomonts appear to be able to survive the reactor's conditions, and if they are released from it with the water outflow, they could hatch in aerobic parts of the RAS.