Medaka, Oryzias latipes complex, display sexual dimorphisms in anal- and dorsal-fin lengths that suggest that females may prefer males with longer fins. However, female preference for longer anal and/or dorsal fins has not yet been described for the medaka. One reason that previous studies have not investigated this relationship may be because variations in male fin lengths within a single population are too small to experimentally detect female preference. In this study, we artificially crossed individuals from two wild populations (Aomori and Okinawa) that differed in male anal- and dorsal-fin lengths to increase phenotypic variation. We then tested female mate preference using these hybrid males. The results of the mating experiments and stepwise multiple regression analyses indicate that anal- and/or dorsal-fin lengths of the males contributed to female preference (i.e., males with longer anal and/or dorsal fins were less likely to be rejected by females). Variation in male standard length did not affect female preference. The evolution of female preference for longer fins in the medaka species complex may be explained by the “sexy son” hypothesis or the direct benefit hypothesis.