show Abstracthide AbstractTrouts of the Salmo trutta species-complex show high morphological and ecological diversity that, along with their very wide distribution, have led to morphological description of 47 extant nominal species, some of high conservation concern. However, many of these species have not been supported by previous phylogenetic studies, which could be partly due to the limited resolution offered by molecular methods previously used. These taxonomic challenges hinder their conservation. The development of next-generation sequencing (NGS) and related analytical tools have enhanced our ability to address such challenging questions. In this study, Genotyping-by-Sequencing (GBS) was used to assess the phylogenetic relationships among Salmo trout representatives throughout their natural distribution in Europe, west Asia, and North Africa.