Seasonal timing of life-history events is often under strong natural selection. The Clock gene is a central component of an endogenous circadian clock that senses changes in photoperiod (day length) and mediates seasonal behaviours. Among Pacific salmonids (Oncorhynchus spp.), seasonal timing of migration and breeding is influenced by photoperiod. To expand a study of 42 North American Chinook salmon (Oncorhynchus tshawytscha) populations, we tested whether duplicated Clock genes contribute to population differences in reproductive timing. Specifically, we examined geographical variation along a similar latitudinal gradient in the polyglutamine domain (PolyQ) of OtsClock1a and OtsClock1b among 53 populations of three species: chum (Oncorhynchus keta), coho (Oncorhynchus kisutch) and pink salmon (Oncorhynchus gorbuscha). We found evidence for variable selection on OtsClock1b that corresponds to latitudinal variation in reproductive timing among these species. We evaluated the contribution of day length and a freshwater migration index to OtsClock1b PolyQ domain variation using regression trees and found that day length at spawning explains much of the variation in OtsClock1b allele frequency among chum and Chinook, but not coho and pink salmon populations. Our findings suggest that OtsClock1b mediates seasonal adaptation and influences geographical variation in reproductive timing in some of these highly migratory species.