Meeting the rising demand for aquatic products requires the production, and subsequent domestication, of new wild animal species (Fontaine et al., 2009). However, breeding new species is characterised by numerous challenges which can impede the sustainability of animal production. Indeed, successful domestication of a novel species is a long-term and difficult process since it implies completing the species life cycle in a human-controlled environment. Moreover, translocations of individuals within and outside the species distribution range can happen when the production and subsequent trade begin. However, unregulated translocations can lead to many conservation concerns such as biological invasion, pathogen spillover, and genetic homogenisation/outbreeding (Lecocq et al, 2016). In this context, knowledge of spatial genetic variability (i.e. differentiation and diversity) patterns is crucial to promote animal production development as well as to mitigate its potential negative impacts on wild populations (Danancher and Garcia-Vazquez, 2011). Indeed, genetically differentiated allopatric populations underwent specific evolutionary histories and could have acquired (through genetic adaptations to local environments) phenotypic specificities which can present different domestication predisposition or socio-economic attractiveness (see for non fish species, Velthuis and van Doorn, 2006). In addition, considering genetic variability patterns is crucial to establish guidelines for trade regulations of the species within its natural range. Despite the potentially valuable integration of intraspecific divergences in incipient species productions and trades, most of current domestication programmes consider species as a unity and disregard inter-populational geographic differentiation. We investigated the genetic variability of a fish species at a nascent stage of its aquaculture production, the European perch (Perca fluviatilis). We characterised the genetic variability across 84 West-Palaearctic sampling sites using four mitochondrial sequences and eight microsatellites. By considering this variability, we aimed at providing (i) guidelines for efficient regulations of the movements of the species within its natural range and (ii) a genetically-based population structure that could be used to highlight units within species which present an interest for production (i.e. best aquaculture performances). Our analyses showed an uneven distribution of the genetic variability across the species distribution range. Based on genetic differentiation, we identified five large geographic scale clusters: European plain, Danube and Alpine Foreland, western and northern Fennoscandia, eastern Europe, and Balkans. These main clusters were further subdivided into several subgroups when analysing population structure with microsatellites. Mapping of genetic diversity highlighted several hotspots across the species range. This spatial pattern of intraspecific diversity implies to develop specific and appropriate regulations of translocations in order to keep the geographic cluster specificities. Moreover, we investigated aquaculture performances of different populations belonging to different clusters through a multifunction and multitrait study using a common-garden approach. We observed similarities between geographic differentiations in genetics and in zootechnical performances (i.e. growth, behaviour, survival). These results are particularly interesting for further investigations of population-specific performances in aquaculture.