Iksookimia longicorpa and Cobitis hankugensis are two species of fish distributed only on the Korean Peninsula. They have a unique reproductive ecology that naturally hybridizes into three widely known unisexual types, maintaining populations of almost all females. In this study, the fine structure of the micropyles of I. longicorpa, C. hankugensis and their hybrids was analyzed to find out how egg–sperm interaction, a common interspecies isolation mechanism, is possible between heterogeneous species. Analysis of 30 eggs from five females of each species revealed that all had one funnel-shaped micropylar region and a manhole-shaped micropyle canal. With the exception of C. hankugensis, which had no spiral grooves or ridges, the rest had counterclockwise spiral grooves and ridges on the micropylar region. All five species, however, showed identical groove patterns for the micropyle canal. The egg size was the largest in HL (one from the C. hankugensis locus with one from the I. longicorpa locus) and the smallest in C. hankugensis. In the hybrids, the HL type had the largest egg and HHL (two from the C. hankugensis locus with one from the I. longicorpa locus) type the smallest. For the diameter of the micropylar region and micropyle canal, the diploid I. longicorpa, C. hankugensis and HL were smaller than those of the triploid. In addition, as the ratio of the canal diameter to the eggs was lower in I. longicorpa than in C. hankugensis, it was confirmed that I. longicorpa has a relatively small micropyle canal compared with C. hankugensis.