Despite a growing economic interest, European perch aquaculture is still limited by several bottlenecks, especially at first life stages (e.g., slow growth rate, high cannibalism rate). Yet, first pieces of evidence suggest that geographic differentiation (i.e. differentiation between wild allopatric populations) can lead to population-specific potential for aquaculture. Some of the European perch aquaculture bottlenecks could thus be overcome by selecting the most efficient population(s) for fish production. This places a premium on the assessment of (i) the likely geographic differentiation in a species of concern and (ii) the potential population-specific performances in captive environment. Here, we investigate potential divergences in aquaculture performances between genetically differentiated allopatric populations of Perca fluviatilis through a multi-trait assessment approach in standardized RAS (re-circulating aquaculture system) environment. First, we use genetic information as a proxy to infer geographic differentiations within the range of Perca fluviatilis. We analyze the genetic variability across 84 West-Palearctic sampling sites using four mitochondrial sequences (1,893 bp) and eight microsatellites using spatial analyses of molecular variance and STRUCTURE analyses. Second, we compare the performances between groups of genetically differentiated populations for several traits important in aquaculture (growth, behaviour, stress resistance, and immunity) through univariate and multivariate statistical analyses. Our genetic analyses show an uneven distribution of the genetic variability of P. fluviatilis across the West-Palearctic. We highlight a two-level population structure: (i) a population structure dividing the species European range in five population groups occurring in five different large geographic areas based on mitochondrial sequences and (ii) a subdivision of these five groups into several subgroups according to microsatellites' analyses. Our preliminary and ongoing analyses show performance differentiations between populations from the five different large geographic areas. Our findings will be helpful to improve rearing programs, overcome bottlenecks in P. fluviatilis aquaculture by considering intraspecific differentiation of the species. This should allow positioning future developments of the species production to the most adapted population(s) to RAS conditions.