Single nucleotide polymorphisms (SNPs) have potential for broad application in population and conservation genetics, but availability of these markers are limited in many non-model species. In this study, genomic and expressed sequence tagged (EST) sequences from closely related salmonids (Chinook salmon, and rainbow trout) were used to design primers for amplification and sequencing of sockeye (Oncorhynchus nerka) and coho (O. kisutch) salmon DNA for SNP discovery. One-hundred and six primer sets were designed and tested for amplification in each species. An ascertainment panel of 32 diverse individuals from each species was used as template for PCR amplification and Sanger sequencing. In total 21,647 bases of consensus sequence were screened in sockeye salmon and 20,784 bases in coho salmon with 93 and 149 SNP sites identified, respectively. Sixty four SNP sites were chosen for assay development and 54 of the assays were validated by comparison of genotype and sequence data (O. nerka = 23; O. kisutch = 31). These validated SNP assays along with 142 other available SNP assays (O. nerka = 103 [126 total]; O. kisutch = 30[61 total]) were used to genotype collections of O. nerka (N = 5) and O. kisutch (N = 4) from various sites in the Columbia River to evaluate the utility of these markers in this region. Results from factorial correspondence analysis (FCA) indicate that these SNP markers are capable of distinguishing O. nerka populations, but O. kisutch collections were less distinct due to their common ancestry.