In this study, the genetic diversity of Eurasian perch Perca fluviatilis was compared between two lakes, Lake Geneva and Lake Neuchatel, which are only separated by 50 km and often used to establish the broodstock for farming. Perch were sampled in six localities in Lake Geneva, and two localities in Lake Neuchatel. Analyses were performed using twelve microsatellites in June 2012 (spawning period) and September 2012 (early autumn). Results revealed that perch populations in Lake Geneva were genetically different than those of Lake Neuchatel. Genetic diversity of perch in Lake Neuchatel (mean number of allele A = 6.91, allelic richness A(r) = 5.19 and observed heterozygosity H-o = 0.607) were significantly higher than for perch in Lake Geneva (A = 6.08 A(r) = 5.86 and H-o = 0.416). Some private alleles were present and characterize each lake population. According to F-ST-pairwise estimates, populations of the two lakes were significantly different. Some hypotheses that may explain this difference are discussed: the nature of the watershed and the anthropic pressures, as fishing pressure and aquaculture practices. Even at a fine-local scale, the choice of the origin of a wild population influences the initial genetic variability introduced in the farming system at the first step of domestication.