The geoduck Panopea globosa is found on the Pacific coast of Baja California south of Bahia Magdalena Bay and throughout the Gulf of California, and sustains a vibrant and growing fishery. Despite morphometric analyses that suggest populations from the Pacific are distinct from those inside the Gulf of California, it is unclear whether populations are connected via larval dispersal and gene flow throughout its range. Thirteen microsatellite loci were used to estimate levels of genetic diversity and to evaluate genetic connectivity patterns among four exploited populations, including clams from the Pacific (Bahia Magdalena) and the Gulf of California (San Felipe, Puerto Peñasco, and Guaymas). Geoducks from Bahia Magdalena showed significant genetic differentiation from populations inside the Gulf of California, particularly when compared with San Felipe and Puerto Peñasco. Gene flow and inferred larval dispersal were found to be predominantly unidirectional, and followed the typical anticyclonic (clockwise) circulation of the northern Gulf of California during late fall and winter when geoducks spawn. San Felipe is located upstream relative to the oceanographic flow and has the largest effective population size. This population also showed evidence of local retention of larvae and may serve as the main source of larvae to downstream populations that show a gradient of reduced diversity and population size along the direction of the prevailing flow. The asymmetry found in connectivity patterns has implications for distributing the fishery effort and no-take zones in the Gulf of California to increase sustainability.