Medaka (Oryzias latipes), an indigenous species in Japan, has decreased in population size in many areas since the first introduction of mosquitofish (Gambusia affinis) in 1916. It is known that predation and aggressive attacks by mosquitofish cause damage to the fins of medaka as well as direct mortality. By experimentally manipulating fin size, we examined the potential effects of damaged anal and caudal fins in male medaka on reproduction. Decreased size of anal fin resulted in a decrease in the number of eggs spawned and the proportion of eggs fertilized. By contrast, decreased size of caudal fin decreased the number of eggs spawned but did not affect fertilization rate. Our results show that damaged anal and caudal fins may give rise to different effects on reproduction in medaka, probably due to the different roles in reproductive behavior.