Yelloweye rockfish Sebastes ruberrimus in the Puget Sound/Georgia Basin (PSGB) region are genetically differentiated from the outer Pacific coast of North America, while canary rockfish S. pinniger show no population structure between these regions. These characteristics helped determine each species¿ status as a distinct population segment (DPS) under the U.S. Endangered Species Act. Here, we explore larval dispersal patterns and test whether these patterns could explain the differences in population structure. We used a 3-D oceanographic model to simulate dispersal of each species¿ larvae from sites inside and outside PSGB for up to 120 days. Dispersal patterns were similar across species and site-specific. Most larvae were found in the same DPS region or management basin from which they were released, but dispersal across boundaries was greatest from release sites nearest the DPS boundary for both species. Dispersal of larvae into the DPS from release sites outside the DPS increased and retention of larvae within the DPS increased with increasing pelagic larval duration, but this was also influenced by a simulated ontogenetic shift in larval depth distribution. The proportion of cross boundary dispersal observed for both species was likely high enough by day 90 to allow gene flow across boundaries, which is consistent with the lack of population structure observed in canary rockfish, but conflicts with the differentiated population structure observed in yelloweye rockfish. Understanding the potential larval dispersal pathways within and across management boundaries is an important step in the successful spatial management and recovery of important and protected species.