Potential for aquaculture can differ among allopatric wild populations of a species of interest. This makes relevant to seek best candidates for fish farming at the intraspecific level. Here, we compare the aquaculture potential among allopatric population groups of the European perch, a species of interest for fish farming. More specifically, we aim at finding population groups with the best performance in larviculture through an integrative approach that allows considering geographic differentiation in domestication processes. A multi-function/trait assessment was performed on three genetically differentiated groups of European perch populations: (i) Danube, (ii) Eastern Europe, and (iii) European Plain. A geographic differentiation was highlighted for six important traits for perch larviculture: survival rate, swim bladder inflation rate, deformity rate, length at hatching, mean of interindividual distances, and change in activity following a stress event. Along with fish farmer-advice-based weighting of the traits, the calculation of an aquaculture potential score allowed identifying the populations from the Danube region as the most interesting to potentially overcome current bottlenecks in European perch larviculture.