Abstract The relationships of Lycopodium and Lycopodiella (Lycopodiaceae) were investigated based on two plastid data sets (rbcL gene and trnL intron) from a representative sample of 21 species. Separate and combined analyses of the data reveal consistent patterns of relationship. There is strong support for monophyly of Lycopodium and Lycopodiella. There is also support for monophyly of species groups or sections sensu Ollgaard (Lycopodium, Diphasium, Magellanica, Complanata, Lycopodiella, and Campylostachys). The combined data provide new evidence of relationships between subgeneric groups. In Lycopodium, section Pseudodiphasium groups with section Magellanica, section Obscura groups with section Diphasium, and section Annotina groups with section Lycopodium. In Lycopodiella, sections Lateristachys and Caroliniana group with section Campylostachys and this group is sister to section Lycopodiella. Tentative calibration of the phylogenetic tree using fossil evidence indicates a minimum age of Early Jurass...