Saxifraga L. is the largest genus in Saxifragaceae and a characteristic component of the herbaceous flora of the temperate and alpine mountains in the Northern Hemisphere. Section Irregulares is a small group of 15-20 species, representing one of the early-diverged lineages in the genus characterized with unique zygomorphic flowers. We used both nuclear internal transcribed spacer and chloroplast DNA regions (psbA-trnH, trnL-F, and matK) to reconstruct its species relationships, estimate divergence times, and infer its historical biogeography. Our phylogenetic results corroborate the monophyly of sect. Irregulares and its sister relationship to sect. Heterisia from North America. The section was well resolved into two lineages corresponding to their morphological features and biogeographic distributions. One represents ser. Stoloniferae including S. stolonifera Curtis and S. nipponica Makino with long-creeping stolons/rhizomes and small petals with spots and the other comprises the remaining taxa (ser. Rufescentes) which lack long-creeping rhizomes. Spots on leaves (abaxially spotted vs. abaxially without spots) and spots on petals (without spots vs. with spots) are inferred to be phylogenetically informative within ser. Rufescentes. Divergence time estimates and ancestral area analysis suggested a western North American origin of sect. Irregulares with migration into East Asia by way of the Bering land bridge in the Middle Oligocene. The development of drying and desertification belt in the late Miocene could have played an important role in the subsequent restriction and separation of the north and south lineages within eastern Asia.

The taxonomy of Selaginella has been historically problematic due to the indistinguishable morphological characters within species complexes. The S. labordei group contains (S. subg. Stachygynandrum) 4–7 species, distributed from the Himalayas to eastern China. The taxonomy of this group was problematic due to few collections that were available to delimitate S. jugorum and S. tibetica, and large variation of the widely distributed S. labordei in different ecological conditions. Here, we re‐evaluate the species delimitation of the S. labordei group using morphological, molecular and cytological data. A total of 55 individuals representing five species of the S. labordei group were investigated using two nuclear markers (26S rDNA, pgiC), one plastid marker (rbcL), as well as 43 plastid‐coding sequences obtained from assembled plastid genomes. Five species are recognized based on the phylogenetic analysis of nuclear genes and plastid‐coding sequences. The plastid genomes phylogeny showed a good resolution at lower taxonomic levels. All the individuals of the broadly defined S. labordei formed a monophyletic group in our analyses of different datasets. However, samples of S. chrysocaulos were strongly supported as non‐monophyletic and were divided into two clades. One clade of S. chrysocaulos is described as a new species, Selaginella parachrysocaulos sp. nov., which is a cryptic species morphologically almost indistinguishable from S. chrysocaulos but with the microspores covered by a honeycomb‐like network microstructure. The nuclear pgiC phylogeny and flow cytometry evidence indicate that some individuals of S. parachrysocaulos may be derived from polyploidization. Based on molecular and morphological evidence, S. sichuanica and S. daozhenensis are treated as synonymous to S. labordei, and S. hengduanshanicola to S. tibetica. Our results uncover the previously mysterious affinities of S. jugorum and S. tibetica, which are members of the S. labordei group.