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Limited approaches exist for studying population connectivity in widely dispersing marine benthic invertebrates. Genetic techniques can provide important insights toward identifying recruitment trajectories. Here, 10 microsatellite loci were used to examine connectivity among Oregon Dungeness crabs ( Cancer magister, Dana, 1852) in the California Current System (CCS) ( n = 801) as well as between Oregon and two British Columbia populations, Alison Sound ( n = 54) and Boundary Bay ( n = 48). Using population-based methods (F-statistics), evidence for weak genetic differentiation was found among 12 sites in Oregon that did not conform to a pattern of isolation by distance.Whereas individual-based methods (kinship analyses) indicated higher than expected relatedness in two Oregon sites, this finding did not help interpret the pattern of genetic differentiation observed among sites in the CCS. Extending our analyses to British Columbia, it was determined that genetic diversity within the Boundary Bay population was comparable to that observed for Oregon, whereas genetic diversity within Alison Sound was considerably lower. Furthermore, genetic connectivity between Oregon and British Columbia was reduced as Alison Sound was genetically distinct from all Oregon sites, whereas Boundary Bay was genetically differentiated from several Oregon sites. In accordance, a Bayesian clustering approach provided support for two genetic groups: (1) Oregon and Boundary Bay and (2) Alison Sound. Kinship analysis revealed a high degree of relatedness within Alison Sound which helps explain the observed pattern of population differentiation. By combining population-based and individual-based approaches, these results demonstrate that connectivity between ocean and fjord-like areas is reduced and may lead to elevated kinship in isolated populations. [ABSTRACT FROM AUTHOR]