The Eurasian and Mediterranean Selaginella helvetica group is one of the taxonomically challenging groups in the cosmopolitan lycophyte genus Selaginella. Species of the S. helvetica group are all small plants with lax strobili composed of more or less isomorphic sporophylls (isosporophylls) that are basically non-resupinate. Owing to the similar and minute morphological characteristics, the inapplicability of chloroplast DNA markers for species delimitation and the lack of range-wide sampling, no comprehensive study has been conducted on these species so far. In this study, we performed phylogenetic analyses based on population-scale sampling of 126 individuals, covering the entire geographical distribution and morphological variation of this group. Five chloroplast (rbcL, psbA, atpI, atpF, atpF-H) and two nuclear DNA regions (26S rDNA, pgiC) were used to explore species diversity of this group. The phylogeny inferred from nuclear DNA datasets revealed nine well-supported monophyletic groups, which provided important evidence for species delimitation and called for taxonomic revision of some taxa. However, in the chloroplast phylogeny, individuals of only three species (S. denticulata, S. helvetica, S. tamamontana) formed monophyletic groups, respectively. We further investigated genome size for each species by flow cytometry and evaluated 21 morphological characteristics of 79 herbarium specimens. MaxEnt analysis was performed to predict the potential suitable distribution of each species. As a result of total evidence, 10 taxa were recognized in the S. helvetica group. The delimitation of S. denticulata, S. laxistrobila, S. nipponica, S. pallidissima, S. prostrata, and S. tamamontana was congruent with previous taxonomical treatments. We reinstated S. shensiensis as an independent species and treated S. longistrobilina as its synonym. Selaginella helvetica (s.str.) is confined to Europe and North Asia, former records of it from the Himalaya-Hengduan mountains represent an independent species (S. jiulongensis comb. nov.). The nuclear pgiC phylogeny and flow cytometry evidence indicated that S. pseudonipponica is an allotetraploid with S. shensiensis and S. nipponica as its parents. Our results highlight that nuclear DNA markers rather than chloroplast DNA markers are more informative in delimitation of closely related species in Selaginella.