A key developmental transformation in the life of all vertebrates is the transition to sexual maturity, whereby individuals are capable of reproducing for the first time. In the farming of Atlantic salmon, unwanted maturation that occurs prior to harvest size has a serious negative impact as it retards growth while severely diminishing flesh quality. Here we report results of two genome wide association studies (GWAS) in Tasmanian animals (derived from North American stock) to map genetic loci that contribute to variation. A total of 2721 fish with trait data describing maturation in the marine environment were genotyped using a custom SNP50 array. Genotypes were also collected from 1846 fish with trait data describing maturation in freshwater. For both experiments, a case-control design lineage regression analysis was performed to identify associated regions. GWAS results suggest a polygenic architecture of both traits. However, the two traits have different architecture as few highly associated SNP were common to both experiments. Further, neither GWAS suggests VGLL3 plays a major role in the two maturation traits as measured in the Tasmanian population. Systematic assessment of the gene content of associated genomic regions revealed genes involved in energy metabolism and brain/gonad functions.