Beaches along Cook Inlet, AK, historically supported commercial, sport, and personal use fisheries for the Pacific razor clam (Siliqua patula). In 2015, east Cook Inlet beaches were closed to sport and personal use harvests, however, due to low abundances of adult clams with concomitant decreases in average length and percentages of large-sized razor clams. Meanwhile, razor clams in west Cook Inlet have not experienced the same decline, and west Cook Inlet beaches remain open to harvest. The universality of the trends in east Cook Inlet suggests post-settlement mortality as a primary driver, but changes in source-sink population dynamics or oceanographic processes may also differentially influence productivity. Given the differences in productivity between east- and west-side beaches, a key question is the degree to which razor clams around Cook Inlet are genetically connected. To answer this question, RAD-seq was used to discover and successfully genotype 44,040 single nucleotide polymorphisms in 37–48 razor clams collected from 11 sites around Cook Inlet and one site on the Alaska Peninsula. Pairwise F_ST estimates indicated a lack of neutral population genetic structure across the sampled range, with no evidence of genetic isolation among samples, between east and west Cook Inlet, or between 2 y classes with sufficient sample sizes, and less than 0.1% of loci were deemed F _ST outliers. Despite the lack of neutral and putatively adaptive variation, these results provide insights into the biological and ecological processes that may influence dispersal, recruitment, and stock productivity among Cook Inlet razor clam aggregations. Moreover, the knowledge gathered can assist resource managers in evaluating harvest strategies for Cook Inlet sport and commercial razor clam fisheries and provides information salient to abundance and demographic survey design.