Species identification and analysis of phylogenetic relationships within the genus Typha are difficult because of the high degree of variability among morphological characters and frequent interspecific hybridization. Traditionally, two sections (T. sect. Ebracteolatae and sect. Bracteolatae) have been recognized within the genus based on the presence or absence of bracteoles in the female flowers. The aims of this study were to reconstruct the phylogeny of Typha using DNA sequence data from nuclear LEAFY and three plastid regions, and to evaluate previous classifications. We sampled nine species from various regions that were each invariant at the molecular level. A parsimony consensus tree recovered three clades in the genus: clade I including T. angustifolia, T. elephantina, T. domingensis, and T. capensis; clade II including T. orientalis and T. laxmanni; and clade III comprising T. latifolia and T. shuttleworthii. Typha minima was found sister to the rest of the Typha species with maximal bootstrap support. The results do not support previous classifications of Typha. Character analysis showed that bracteole loss, spatulate stigma, lack of a gap between staminate and pistillate inflorescences, and monad pollen are derived characteristics in Typha.