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The lipid-rich copepodNeocalanus flemingeriis abundant throughout the subarctic Pacific, with a biogeographic range that includes the open ocean, marginal seas and fjord systems. Two distinct genetic variants have been reported based on differences in size: the ‘small form’, with a 1 yr life cycle, is found throughout the region, and the ‘large form’, with a 2 yr life cycle, is found in the western Pacific, where it is most abundant in the Sea of Okhotsk. Using a molecular approach, this study examined the genetic composition ofN. flemingeripopulations in the Gulf of Alaska from multiple stations over a 9 yr period. This is the first report of the occurrence of the large form in the eastern Pacific, where it exhibits a significant presence in fjord systems. However, in this region, both the small- and large-formN. flemingerihave annual life cycles. Collections from nearshore to offshore locations over multiple years indicated both interannual and spatial differences in the relative proportion of the 2 variants. Our results show that the forms inhabit overlapping yet distinct habitats, potentially due to adaptation to contrasting environmental conditions.