In fishes, maternal size typically influences the number of offspring. Although this size-fecundity relationship often varies among species and is considered to be a consequence of the coevolution of life-history traits, the genetic basis of such size-fecundity relationships remains unclear. We explored the genetic basis underlying this size-fecundity relationship in two small medaka species, Oryzias latipes and O. sakaizumii. Our findings showed that O. sakaizumii has a higher fecundity than O. latipes, and quantitative trait locus analysis using interspecific F₂ hybrids showed that chromosome 23 is linked to the size-fecundity relationship. In particular, the genes igf1 and lep-b in this region are known to be associated with life-history traits. Because O. sakaizumii is distributed at higher latitudes and has a shorter spawning season than O. latipes in the wild, we propose that adaptation to high latitudes is responsible for the relatively high fecundity observed in O. sakaizumii. We also discuss the potential ecological ramifications by the evolution of increased fecundity in this species.