Equisetum is a genus of 15 extant species that are the sole surviving representatives of the class Sphenopsida. Chloroplast DNA sequence data were used to examine the monophyly of the two accepted subgenera (Equisetum and Hippochaete) and the putative basal position of Equisetum giganteum. A plastid DNA region that includes rps4 was sequenced for all species of Equisetum. Phylogenetic analyses using parsimony, likelihood or posterior probability criteria, all support the following inferences: (1) Equisetum bogotense is basal within the genus; (2) all other species group in two major sister clades: (i) the rest of subgenus Equisetum (7 species) and (ii) subgenus Hippochaete (7 species). On the basis of the present phylogeny, bisexuality would not be the ancestral state in the Equisetum genus, but characters shared among species of the subgenus Equisetum, such as superficial stomata and protruding antheridia, could be ancestral in the genus.