Dynamic marine environments can shape complex spatial and temporal patterns in the population connectivity of marine species. A genotyping-by-sequencing (GBS) approach was used to examine fine-scale spatial and temporal genomic variation among Dungeness crab (Cancer magister) larval recruits (megalopae stage) sampled in the California Current Ecosystem (CCE). Samples during expected- and late-season recruitment time periods within two consecutive years (2017 and 2018) at two sites in Oregon, USA (Yaquina Bay and Coos Bay) were compared. Given the high economic and social value of the Dungeness crab commercial fishery along the west coast of North America, it is important to understand the population connectivity of the species in order to maintain a sustainable fishery in the face of climate change and changing ocean conditions.