The Southeastern District Mainland (SEDM) commercial salmon fishery occurs in the Alaska Peninsula Management Area, Westward Region, is regulated based upon a board-approved management plan, and has allocative constraints between June 1 and July 25 based upon the abundance of Chignik River sockeye salmon. Significant controversy has persisted between SEDM and Chignik Management Area fishermen concerning the estimate of Chignik-bound sockeye salmon harvested in the fishery. Western Alaska Salmon Stock Identification Program used mixed stock analysis (MSA) to determine stock of origin of sockeye (and chum salmon) in commercial and subsistence fisheries throughout Western Alaska from 2006 to 2009. As a result of low returns to the Chignik River during these years, the SEDM fishery was often closed and few samples were collected for analysis. This study was designed to fill in those holes and estimate stock proportions and stock-specific harvests of sockeye salmon sampled from the SEDM fishery. Genetic samples were collected from the fishery over a three-year period (2010–2012). A total of 17,078 sockeye salmon tissue samples were collected from three locations in SEDM. Of these, 8,357 samples were ultimately genotyped to represent 21 area-temporal strata. An updated baseline with an important local stock defined as a separate reporting group (stock) performed well for MSA. Chignik River sockeye salmon dominated catches during 2010–2012, contributing 65%, 67%, and 66% of the annual SEDM harvests sampled for MSA (excluding some Northwest Stepovak Section harvests in July). These percentages were less than the expectation in regulation, and the local Orzinski Lake stock also contributed less than expected to SEDM harvests sampled for MSA. These results provide the most comprehensive estimates of stock composition and stock-specific harvests of sockeye salmon in the SEDM area, supplement previous studies, and should inform fishery management and regulatory decision makers.