Although evidence of associations between genetic diversity and fitness in wild species has been published, the lack of a comprehensive review across species and the existence of contradictory results have led to scepticism remaining about its existence and importance in natural populations. In this study, the relationship between genetic diversity at six microsatellite loci and condition factor (a fitness related trait) was investigated at the population level in both Flemish and German populations of the European bullhead (Cottus gobio). A significant positive correlation was observed between genetic variability and the condition factor in Flemish but not in German bullhead populations. Environmental conditions such as conductivity of the water seemed more important in determining the condition factor of these latter populations. Regardless of the underlying mechanism(s) responsible for the different relationships, the results of this study suggest that both genetic and environmental variables can influence condition factor of bullhead populations.