Next generation sequencing data can be used for rapid identification of genetic markers linked to phenotypes of interest for use in conservation, resource management or breeding. Here we report on the use of genotyping by sequencing (GBS) to develop SNP markers linked with phenotypic sex and with a transgenic construct in coho salmon (Oncorhynchus kisutch). Associations between phenotypes and genotypes were confirmed using high-resolution melting analysis (HRMA). A total of 56 SNPs were associated with phenotypic sex after analysis with the software TASSEL. Concordance between phenotypes and genotypes were tested for 28 SNPS, and of these, seven had moderate to high concordance across test populations. However, only one SNP showed 100 % concordance across all test populations. Fifteen SNPs were associated with the transgenotype using a TASSEL analysis of the GBS data; of these, four showed moderate to high concordance with the transgenotype using HRMA. This type of approach could be used to identify SNPs associated with phenotypes of interest in species with few previously developed genetic resources.