Population of Gnathopogon (Cypriniformes, Cyprinidae) from a dammed reservoir Lake Ono in Yamaguchi Prefecture is estimated to be a hybrid swarm between brookletdwelling G. elongatus and pelagic planktivorous G. caerulescens of Lake Biwa. Alleles on a protein-coding locus Prot-3^* are nearly exclusively fixed to ^*a and ^*b in G. elongatus and G. caerulescens respectively. Gnathopogon from Lake Ono, on the other hand, has both of homozygote and heterozygote genotypes of the alleles in its population, namely aa, ab and bb. Morphological comparison revealed that there are no differences in relative lengths and meristic counts among three genotypes of Gnathopogon from Lake Ono, which supports the hybrid swarm theory.