Ficus (Moraceae) is a well-known group with specific pollination mutualisms, and hybridization is considered to be rare. Here, we report the presence of interspecific hybrids between Ficus pumila L. and F. thunbergii Maxim. on Okinoshima, a small island offshore of Shikoku, western Japan. AFLP (amplified fragment length polymorphism of genomic DNA) data suggested that more than one-fourth of individuals of morphological F. pumila were assigned as intermediate genotypes, suggesting hybrids. The hybridization between the two species was introgressive and unidirectional from F. thunbergii to F. pumila. The findings of this study, combined with other previous reports, suggest that the breakdown of mutualistic systems can occur in isolated populations such as those on islands.