Objective The cell cycle regulator MCM5 plays a critical role in the initiation of DNA replication and also functions in transcriptional regulation. However, its role in embryonic development is largely unknown. The aims of this study were to examine the expression pattern of mcm5 in early zebrafish embryos and investigate its function in somitogenesis. Methods First, the expression pattern of mcm5 was analyzed by whole?mount in situ hybridization in zebrafish during early embryonic development. Then, antisense morpholinos (MOs) were injected into embryos to disturb Mcm5 protein expression and the associated defects of somitogenesis were examined. Results MCM5 is a maternal factor that is ubiquitously expressed from the one?cell to early?somite stage. mcm5 transcripts are restricted to the tailbud, somite, and head at later stages. These result indicate the possibility that mcm5 is involved in somitogenesis. mcm5 morphants exhibit a shortened anterior?posterior axis and smaller eyes compared with control embryos. In situ experiments further revealed that some genes crucial for somitogenesis are downregulated during somitogenesis when mcm 5 is depleted. Conclusions mcm5 is involved in zebrafish somitogenesis.