Asplenium is one of the most species-rich genera of ferns. While ubiquitous polyploidy and hybridization events, as well as vast distribution ranges, contribute to its remarkable diversity, these facts also lead to extreme classification difficulties. The A. exiguum complex is a natural morphological assemblage of taxa sharing part or all ancestral genomes due to polyploidy and hybridization. Consisting of 4 to 13 taxa mainly distributed in the Sino-Himalayan region, taxonomic issues of this complex have been debatable for a long time. Here, we collected 49 samples representing the majority of the recognized taxa and reconstructed phylogenetic trees using two plastid loci (rbcL, rpl32-trnP) and three nuclear loci (pgiC, SQD1, nrDNA). Evidence from ploidy, macro- and micromorphology, geographical pattern, and ecological niche was also integrated to illuminate the species boundaries and evolutionary history within the complex. According to our investigation, six taxa, including two diploid species (A. barkamense, A. lushanense), three tetraploid species (A. exiguum, A. glenniei, A. nesii), and one triploid nothospecies (A. ×mickelii), are accepted. Asplenium barkamense, which used to be treated as a synonym of A. nesii in Flora of China, is an independent species and the common diploid progenitor of autotetraploid A. nesii and allotetraploid A. glenniei. Moreover, A. glenniei (= A. yunnanense), widespread in the subtropical and temperate regions of East Asia and occasionally seen in the southwestern United States, Mexico, and northern Guatemala of North America, is an allotetraploid originated from A. barkamense and A. lushanense, whereas A. exiguum, known with a narrow distribution in tropical Asia, is a putative autotetraploid offspring of A. lushanense. Therefore, A. glenniei is restored as an independent species from A. exiguum. Asplenium ×mickelii is supported as a sterile hybrid of A. lushanense and A. glenniei. In addition, our study suggests that the majority of speciation events in the complex probably took place in the Hengduan Mountains, where complicated orogenic activities and climatic oscillations facilitate geographic isolation and polyploid establishment. The two tetraploids, A. nesii and A. glenniei, adapted to distinct climate conditions and colonized wider ranges compared to their parents.