Uncertainty about the magnitude, frequency, location, and timing of the nonlocal harvest of sockeye and chum salmon in Western Alaska fisheries was the impetus for the Western Alaska Salmon Stock Identification Program (WASSIP). The project was designed to use genetic data in mixed stock analysis (MSA) to reduce this uncertainty. A baseline of allele frequencies is required for use in mixed stock analysis to estimate the stock of origin of harvested fish. The single nucleotide polymorphism (SNP) baseline for chum salmon Oncorhynchus keta to be used for MSA in WASSIP is in a state of perpetual improvement. To meet the standards set by the Advisory Panel (AP) for increased resolution more emphasis was placed on selecting markers to distinguish among regional areas within Coastal Western Alaska (CWAK). Here we describe the process that we intend to use to select the set of 96 SNPs that maximizes the likelihood of providing the resolution necessary to meet the objectives of WASSIP.