To investigate the phylogeny of early lycopsids, cladistic analyses using both parsimony and Bayesian approaches are presented, with a data matrix of 33 morphological characters across 25 taxa. The resulting parsimony and Bayesian trees showed overall similarities in tree topologies. In the Bayesian tree, the Protolepidodendrales and the heterosporous lycopsids are recognized as two monophyletic groups, and within the latter group, the Isoetales sensu lato forms a subclade. This topology implies that the acquisition of a ligulate character evolved twice in the lycopsids, once in the protolepidodendralean Leclercqia Banks et al., and once in the heterosporous lycopsid clade. Phylogenetic positions of several lycopsid plants previously reported from the Mid-Upper Devonian of South China, which have uncertain ordinal affinities, were estimated by the cladistic analyses; cf. Longostachys Xue et Hao, Longostachys Zhu et al., Monilistrobus Wang et Berry, and Yuguangia Hao et al. fall well within the Isoetales clade, as earliest members of this order, while Minostrobus Wang and Wuxia Berry et al. are nested within the basal part of the heterosporous lycopsids. Bayesian analyses are a very useful approach in systematic studies and can be applied in analyzing paleobotanical data sets as well.