Population surveys using molecular markers often find that heterospecific mtDNA haplotypes are distributed asymmetrically between species. It is ordinarily interpreted that hybrids are produced more successfully by one species than by the other. Here we show that this simple interpretation can be wrong and fails in revealing true evolutionary history. Bradybaena pellucida (BP) is indigenous to Japan and B. similaris (BS) is alien. Our haplotype analysis detected heterospecific haplotypes in more populations in BP than in BS. This suggests that mtDNA may leak from BS to BP more easily than from BP to BS, through better hybrid production by BS. Against this prediction, however, we found that through simultaneous reciprocal mating between the two species, BP produces hybrids but BS does only rarely. BS does not produce hybrids in effect because BP ceases copulation before inseminating BS. We also found that BS does not reproduce even in backcross with hybrids, while hybrids do. Our haplotype network analysis indicates that BS haplotypes are widely distributed in BP populations because founders of BP have been carrying over BS mtDNA in recent increases of distribution range after rare introgression, but not because of frequent hybridization.