Present research suggests that phenotypic variations and consequent potential differences in suitability for commercial culture are more likely to occur among genetically diverse populations. We investigated diversity in traits important to aquaculture and assessed genetic differentiation based on four mitochondrial markers in three European populations of Perca fluviatilis. Using a transplant approach to standardize conditions and minimize environmental effects on phenotype expression, we compared survival, cannibalism, growth rate, growth heterogeneity, and specific growth rate of the populations to assess whether difference in aquaculture performance (i.e. expression of phenotypical traits that facilitate the rearing of fish and impact the productivity of the farming) is more likely between genetically differentiated populations than between genetically similar populations. We found key traits of performance to differ among allopatric populations, suggesting value in considering geographic source of broodstock. The largest aquaculture performance disparities were observed among genetically differentiated populations. Some lesser differences were observed between allopatric genetically similar populations, possibly the consequence of pre-collection environment, or transgenerational effects.