We investigated the relationship between vertebral number variations and spawning time of chum salmon Oncorhynchus keta in the Chitose- and Izari Rivers, Hokkaido Island, Japan. The means of vertebral number in early-spawning populations were higher than those of late-spawning populations in both rivers. A similar trend was observed in juveniles that were derived from different spawning groups in the Chitose River and reared under common conditions. In addition, the means of vertebral number in chum salmon fry captured in the early-sampling season (January and February) were higher than those of the late-sampling season (April) in the Izari River. These results suggest that variations of vertebral number in chum salmon adults and fry are affected by spawning time, and that the variations are originally caused by genetic factors.