Brown trout is a salmonid fish with a natural range extending throughout western Eurasia and North Africa. Due to its commercial value, it has also been introduced worldwide. In continental Croatia, introduced trout of the Atlantic lineage hybridizes with native trout of the Danubian lineage, threatening the native genetic diversity. The geometric morphometrics approach was used in this study to analyse changes in shape between native trout, introduced trout and their hybrids, classified a priori by molecular phylogenetic analyses. A total of 19 landmarks and semi-landmarks were used to capture the shape of 92 trout individuals belonging to two lineages and their hybrids. Canonical variate analysis and discriminant function analysis were used to analyse and describe shape variation. A significant difference was found between the shape of the Atlantic lineage trout and both Danubian lineage trout and hybrids, with the most prominent differences in body depth, head length and eye size. No statistically significant shape differences were observed between Danubian lineage trout and the hybrids. The observed significant differences in shape could be the result of genetic diversity or trout phenotypic plasticity. Further studies are needed to clarify the origin of this variation in shape.