Abstract Background Cold tolerance during embryonic development, especially blood circulation is important for growth in poikilothermic animals. Medaka ( Oryzias latipes ), has cold tolerance and is distributed in the highest latitudes occupied by the genus Oryzias . Regarding cold tolerance in embryogenesis, Hd-rR strain belonging to the southern Japanese (S.JPN) group showed arrhythmia when the embryo was exposed to 15 °C in the heartbeat initiation period (st. 24), whereas the embryo of Odate medaka, which belongs to the northern Japanese (N.JPN) group, showed stable heartbeats. Results In this study, to verify the sensitivity to low temperature in the medaka wild populations, heartbeat intervals of st. 24 embryos derived from three N.JPN, eight S.JPN, and two western Korean/Chinese (W.KOR) populations were investigated at an arbitrary temperature range of 12–15 °C. There was no significant difference in the mean values of the heart rates and the coefficient of variation (CV) of interbeat intervals in the N.JPN, S.JPN, and W.KOR groups. A temperature dependency of the CV within 12–15 °C was observed only in five S.JPN specimens, whereas three S.JPN, the N.JPN and the W.KOR specimens showed no alteration in CV with temperature. Temperature dependency of the heart rate was also varied in the S.JPN specimens. Conclusions These results suggest that the temperature dependency of the CV under 12–15 °C during the heartbeat initiation period is a variation within the S.JPN after the divergence from the N.JPN.