Larval rearing is a crucial step in fish production. However, issues in larval production, such as low growth/survival rate, impede the aquaculture development of many species including Perca fluviatilis. Since allopatric populations of P. fluviatilis exhibit different growth rates for first-life stages, basing fish stocks on populations displaying optimal features in aquaculture conditions could overcome some of these issues. Here, we (i) compare the growth rate in standardised re-circulating aquaculture system conditions and (ii) assess the genetic differentiation using four mitochondrial markers between seven allopatric populations. Our results confirm that key features for aquaculture can vary at the intraspecific level. However, we do not highlight any clear aquaculture trait differences related to genetic differentiation. Therefore, we cannot assess the genetic basis of growth rate differentiation between populations. This paves the way to future studies on aquaculture performances of genetically distinct populations in P. fluviatilis.