The Asplenium pekinense complex mainly comprises one diploid, A. sarelii Hook. (rare), one autotetraploid, A. pekinense Hance (best known and very common), and shares two allotetraploids, A. anogrammoides Christ (common but often misidentified) and A. altajense (Komarov) Grubov (rare and endemic) with the A. varians complex. The latter is further constituted by two diploids, A. tenuicauleHayata (widespread) and A. semivarians Viane & Reichstein (rare), as well as other three tetraploids, A. kansuense Ching (barely known), A. varians Wallich ex Hooker & Greville (well‐known, relatively common, and morphologically variable), and A. kukkonenii Viane & Reichstein (rare and often misidentified). These two species complexes are notorious for their taxonomic difficulty based on general morphology, which is mainly caused by their history of reticulate evolution. Here, we collected most species within the two complexes, and obtained ploidy information by spore size measurement and flow cytometry investigation. Phylogenetic analyses using DNA markers representing maternally inherited chloroplast and biparentally inherited nuclear genomes helped to reconstruct the reticulate evolution history. The present results support previous hypotheses that A. sarelii is the ancestor of both A. pekinense and A. anogrammoides, as well as that A. tenuicaule is the common progenitor of A. anogrammoides, A. varians, and A. kukkonenii. We also unraveled the autotetraploid origin of A. kansuense from A. tenuicaule for the first time, and found that A. altajense shares essentially identical genomes with A. anogrammoides.