The pikeperch is a freshwater/brackish water fish species with growing interest for Euro-
pean aquaculture. Wild populations show signs of decline in many areas of the species natural range
due to human activities. The comparative evaluation of genetic status in wild and domesticated
populations is extremely useful for the future establishment of genetic breeding programs. The main
objective of the present study was to assess and compare the genetic variability of 13 domesticated
populations from commercial farms and 8 wild populations, developing an efficient microsatellite
multiplex tool for genotyping. Partial cytochrome b gene sequences were also used to infer phylogeo-
graphic relationships. Results show that on average, the domesticated populations do not exhibit
significantly lower levels of genetic diversity compared to the wild ones and do not suffer from
inbreeding. Nuclear data provide evidence that pikeperch populations in Europe belong to at least
two genetically differentiated groups: the first one is predominantly present in Northern Europe
and around the Baltic Sea, while the second one comprises populations from Central Europe. In
this second group, Hungarian origin populations constitute a differentiated stock that needs special
consideration. Aquaculture broodstocks analyzed appear to contain fish of a single origin with only a
few exceptions.