AbstractThe lycophyte genusSelaginellaalone constitutes the family Selaginellaceae, the largest of the lycophyte families. The genus is estimated to contain 700–800 species distributed on all continents except Antarctica, with highest species diversity in tropical and subtropical regions. The monophyly ofSelaginellain this broad sense has rarely been doubted, whereas its intrageneric classification has been notoriously contentious. Previous molecular studies were based on very sparse sampling ofSelaginella(up to 62 species) and often usedDNAsequence data from one genome. In the present study,DNAsequences of one plastid (rbcL) and one nuclear (ITS) locus from 394 accessions representing approximately 200 species ofSelaginellaworldwide were used to infer a phylogeny using maximum likelihood, Bayesian inference and maximum parsimony methods. The study identifies strongly supported major clades and well resolves relationships among them. Major results include: (i) six deep‐level clades are discovered representing the deep splits ofSelaginella; and (ii) 20 major clades representing 20 major evolutionary lineages are identified, which differ from one another in molecular, macro‐morphological, ecological and spore features, and/or geographical distribution.