Acrorumohra subreflexipinna, an endemic fern of Taiwan, has been suspected to be a hybrid species. The aims of this study were to detect possible multiple origins of this species, determine the genetic variation in different populations, and clarify their lineages. One nuclear and three organellar DNA fragments were sequenced to determine parentage of this putative hybrid and to examine genetic differentiation among populations. Sequence data support the conclusion that A. subreflexipinna arose from the hybridization of A. hasseltii and A. diffracta, and the hybridization was uni-directional, i.e., based on the assumption of maternal inheritance in organellar DNA, the former was its maternal species while the latter was its paternal source. A convincing interpretation is that the female gametes of A. hasseltii gametophyte could be fertilized by the male gametes from apogamous A. diffracta. Unique nuclear alleles present in different populations of A. subreflexipinna and A. hasseltii demonstrated that hybridization occurred many times independently. The nuclear haplotypes present in A. subreflexipinna were subsets of those found in the parental species, and A. subreflexipinna always had lower haplotype diversity than A. hasseltii at sympatric sites. Our results show that any genetic variation of A. subreflexipinna came from its parents and that it maintains this significant genetic variability because of recurrent hybridization.