Plastome structure, evolution, and phylogeny of Selaginella

•59 plastomes representing 51 species covering all six subgenera and 18 sections of Selaginella except two are sampled.•The enigmatic Sinensis group is included for the first time in a plastome study.•Gene contents and plastome structures in Selaginella vary lineage-specifically.•All infrageneric taxa are well supported in the plastome phylogeny.•Even the concatenated plastomes could not well resolve the relationships in Selaginella with confidence.