This study evaluated the taxonomic status of trout populations from Göksu River in the Mediterranean Basin of Türkiye using an integrated approach combining morphological and molecular data. Comprehensive morphometric and meristic analyses on twenty specimens, along with phylogenetic studies based on Cytb, revealed this population to be a new species. This species forms a monophyletic group within the Adriatic lineage.Population structure analysis for K = 9 revealed nine genetic clusters corresponding to known species and lineages, with no evidence of admixture. This finding suggests strong reproductive and geographic isolation and long-term independent evolutionary processes. The clear concordance between genetic clustering and taxonomic classification provides molecular validation of species boundaries and emphasizes the need to consider each lineage as an independent Evolutionarily Significant Unit (ESU).Supporting these results, genome-wide SNP data also revealed a distinct cluster corresponding to the newly described species and other native trout populations. Salmo semae sp. nov. morphologically distinguishes itself from neighboring Salmo species by having fewer black spots (< 44) confined to the upper lateral line, fewer red spots (< 62) distributed along the mid- and upper lateral line, and consistent spot numbers throughout the growth stages.The species is distributed exclusively in Göksu River and its tributaries and faces potential threats such as overfishing and rainbow trout ( Oncorhynchus mykiss ) aquaculture. This research provides important information about the unique and highly endemic salmonid diversity in Türkiye and highlights the importance of protecting this diversity.