We analysed the genetic variation of the gudgeon Gobio sakaryaensis (Teleostei: Cyprinidae), which is endemic to a subbasin which has been isolated from the Sakarya watershed since the late Pliocene for at least two million years. From the 8 allozyme loci studied, more than half show heterozygote deficiency. Based on tests of selective neutrality, we conclude that the levels of deficiency can be accounted for by genetic drift. Big differences in the frequency between allelic classes at individual loci, an apparent indication of fixation, support this inference. We suggest that hydrogeological isolation is the reason for the genome of the Gobio sakaryaensis population to have evolved mainly by genetic drift.