The phylogenetic relationships of Lycopodiaceae, and specifically the relationships among epiphytic Huperzia, were investigated by means of a cladistic analysis using plastid rbcL gene sequences. Huperzia species are partitioned into neotropical and paleotropical clades, a result that is incongruent with traditional morphology based taxonomy. The rbcL data corroborate an earlier study based on tmL intron and tmL-trnF spacer sequences. Together, these two molecular studies provide strong evidence that the diversification of epiphytic Huperzia is a comparatively recent phenomenon (Late Cretaceous-Tertiary), and that there has been widespread morphological convergence in epiphytes throughout the tropics.