On a small Japanese island, Sado-ga-shima, we identified a frog that differs from Rana rugosa by having a deep yellow coloration of the abdomen and ventral surfaces of the legs. We tentatively refer to it as “yellow morphotype.” To identify any mechanisms of reproductive isolation from R. rugosa, allopatrically distributed on the same island, we artificially crossed the two types and examined the developmental capacity, sex-ratio, and inner-structure of gonads and fertility in the F1 hybrid offspring. Almost all of the reciprocal hybrids became males with a very low abundance of sperm in the testes and show an extremely low fertility when backcrossed to the females of either type. We conclude that the yellow morphotype is reproductively isolated from R. rugosa through all hybrid maleness with scarce fertility and, therefore, presents a species new to science.