In most fishes, the number of offspring increases with maternal body size. Although this size‐fecundity relationship often varies among species as a result 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, including somatic growth, gonad maturation, and progeny numbers in various taxa. Because O. sakaizumii is distributed at higher latitudes and has a shorter spawning season than O. latipes in the wild, we propose that the relatively high fecundity observed in O. sakaizumii is an adaptation to high latitudes. We also discuss the potential ecological ramifications associated with the evolution of increased fecundity in this species.