Ephoron shigae is distributed in Far East Russia, Korea and Japan, where it inhabits rivers, streams and lakes. Although this mayfly is a geographically parthenogenetic species, unisex populations have been observed only in Japan. We aimed to answer the following three questions: (i) whether there is a unisex population of E.shigae in Korea; (ii) whether migration and gene flow exists between E.shigae populations in Korea and Japan; and (3) whether E.shigae populations are fragmented in Korea because of mountains running to the north and south. We observed 20 populations across Korea and investigated the sex ratio in 12 populations. Our results showed that all the populations were bisex, and we believe that there is no unisex population of E.shigae in Korea. In addition, we examined the genetic structure of E.shigae in Korea by using the COI gene. The results showed that the Korean populations were clearly divergent from the Japanese populations; the level of genetic distance between the Korean and Japanese populations was interspecific rather than intraspecific. Therefore, parthenogenetic populations of E.shigae probably belong to unisex populations that originated in Japan, while the individuals would have not migrated to Korea. The Korean populations did not show clear fragmentation by geographic barrier, although this mayfly with extremely short adult stage (up to 2h) could be a comparatively strong disperser across Korea.