Objectives To optimize host-to-host transmission, digenean trematodes (parasites) synchronize their cercarial emission patterns with the aquatic activities of their vertebrate hosts. Schistosoma mansoni has a strictly diurnal shedding pattern involving two circadian chronotypes: an early shedding pattern with a mean peak occurring at 11:00 h and a late pattern with a mean peak occurring at 16:00 h. We analysed the cercarial emergence pattern of three schistosome populations from Oman where S. mansoni is resurgent. Methods For each schistosome population, the cercarial emergence pattern was assessed hourly over several days. Because we identified a new chronotype hitherto unknown in S. mansoni, we undertook taxonomic characterization based on egg morphology and mitochondrial DNA sequence (COX1). Results Taxonomic characterization revealed that the three schistosome populations belong to the species S. mansoni. Hence, this is the first report of this species exhibiting a nocturnal chronotype, with the mean peak occurring at 20:00 h. We interpreted the new chronotype as being the result of a lateral transfer of S. mansoni from humans to Rattus rattus. Conclusion The cercarial emergence pattern of S. mansoni from Oman is circadian, exhibiting either a diurnal or a nocturnal phenotype.