Lepisorus inaequibasis is thought to be of hybrid origin due to its leaf shape and sporangia being intermediate between those of its putative progenitors. Subsequent molecular studies have supported its hybrid origin, but its progenitors have not been determined. Here, we performed molecular phylogenetic analysis, flow cytometry (FCM), morphological character observation, and ecological niche modelling (ENM) to elucidate the origin of L. inaequibasis. The phylogenetic trees inferred from single‐copy nuclear genes (pgiC and gapCp “short”) confirm the hybrid origin of L. inaequibasis from Lepisorus waltonii and Lepisorus jakonensis. Chloroplast DNA (cpDNA) phylogeny indicates that L. jakonensis is the maternal progenitor. All populations of L. inaequibasis share a single cpDNA haplotype identical to the lineage of L. jakonensis in the central Himalayas; thus, we hypothesize that L. inaequibasis originated in the central Himalaya region and dispersed to east Himalaya and Hengduan Mountain regions. Based on FCM, L. inaequibasis is tetraploid, while its progenitors are diploid. Principal component analysis of rhizome scales and observations of sporangial annuli indicated a high degree of morphological similarity between L. inaequibasis and its paternal progenitor species, L. waltonii. The ENM results showed that L. inaequibasis has a relatively high niche identity value with L. waltonii. Therefore, we conclude that L. inaequibasis is an allotetraploid that originated through hybridization between the diploid species L. waltonii and L. jakonensis. This allotetraploid species shows clear paternal bias in both its morphological characters and its ecological niche.