Based on ecological and behavioural studies it has been assumed that Eurasian perch (Perca fluviatilis) within one lake may not represent one panmictic population, but that they are subdivided into subpopulations. In order to investigate the genetic substructuring of populations, we used gene frequencies of five microsatellite loci to compare perch from six different sites from Lake Constance, Germany, and as outgroups perch from the lake Grosser Vätersee, Berlin, and two Swiss lakes, Lake Zurich and Lake Walensee. We examined whether homing behaviour of subadults to the spawning sites of their parents occurs and whether philopatric behaviour of adults results in significant population genetic substructuring. The distribution of genetic variation revealed two major, genetically distinct populations in Lake Constance: one in the eastern part of the lake and another in the western part (GST=0.07). Within each of these two populations, no further genetic substructuring, nor any indication of inbreeding could be detected, either because genetic exchange was sufficiently high or because the time since separation has been too short. Homing behaviour of subadults to parental spawning sites after having spent several weeks of their life cycle in the pelagic zone could not be detected. Instead, subadults stay within either the western or the eastern region of the lake. There is evidence that some shoals contain full- and half-sibs. Despite females spawning in close proximity to each other, some siblings stay together. This might suggest that perch possess kin preferences and kin recognition.