Adiantum meishanianum is an endemic species distributed only in Meishan village, Kaohsiung, Taiwan. Because its sporangia contain only abortive spores, A. meishanianum has been regarded as having a hybrid origin, presumably with A. caudatum, A. malesianum, and A. philippense as the putative parents. The aim of this study is to confirm the hybrid origin and determine the parental lineages of A. meishanianum by examining cytology, reproductive modes, and using molecular phylogenetics. We found that the sequences of two chloroplast regions, rps16-matK intergenic spacer and the matK gene, are identical between A. meishanianum and A. malesianum, suggesting A. malesianum is the maternal parent. The nuclear phylogeny reconstructed based on the low-copy marker, CRY2 first intron, reveals that A. meishanianum has three types of sequences: one type groups with sequences of sexual diploid individuals of A. philippense and the other two group with sequences of the sexual tetraploid A. malesianum, indicating that A. philippense is the paternal species. Our data further imply that the extant A. meishanianum probably originated from a single hybridization event, and its rarity is likely due to the limited distribution of the paternal parent.