Recent study demonstrates the female mate choice in medaka fish, which shows the female preference towards the familiar male. The result indicate the possible individual recognition mechanism in medaka, even when the fish are inbred for generations and homogeneous to each other. We therefore examined which cues were used for medaka individual recognition. We presented female medaka (1)visual cues, (2)olfactory cues, (3)visual and olfactory cues from the same male and (4)visual and olfactory cues of different males, and found cross-modal cognition in medaka. Both visual and olfactory cues were used for targeting familiar male, however, visual cues were more dominant than olfactory cues. When both visual and olfactory cues from different males were presented to the female, they chose the familiar visual cue instead of the olfactory cue. We further tested which parameter were used for visual recognition, including motion and appearance (frontal and side). The results suggested there was no significant difference in motion cues between individual medaka fish, and with motion cues alone cannot arise individual recognition. No difference was shown when presenting frontal or lateral image. We demonstrated cross-modal individual recognition in medaka, and the importance of phenotypic cues in social perception. We aim to find the neural mechanisms underlying individual recognition in medaka for future studies.