The tropical carnivorous pitcher-plant family, Nepenthaceae, is represented by the single dioecious genus Nepenthes. Whilst South East Asia represents the centre of diversity of the group several species have disjunct biogeographical distributions. Due to the highly polymorphic nature of Nepenthes and its distinct lack of discrete morphological characters no revision to date has been able to construct a phylogenetic classification. To address this issue, this study analyses nucleotide sequences from two independent regions, including chloroplast DNA (the trnL-F intron and intergenic spacer) and the nontranscribed spacer region from nuclear DNA (5S-NTS), together with a suite of morphological characters traditionally used to describe and group species. A total of 87 species are represented with the objectives of i) testing the monophyly of the genus and constructing a hypothesis of species relationships, ii) evaluating the taxonomic circumscription of poorly known species and iii) investigating character evolution and biogeographic patterns. In addition, for 25 species, multiple accessions were sequenced. Two artificial hybrids (of known sexual parentage), representing three geographically and taxonomically distinct species, were also included to test prevalent theories of hybrid origin and maternal inheritance. Cladistic analyses of these data strongly support the monophyly of the genus in which the disjunctly distributed species (including the easterly Nepenthes danseri from Waigeo Island and Halmahera) were found to form a grade while the South East Asian taxa form a clearly monophyletic group. Incongruence was found between the phylogenetic histories inferred from independent genetic markers and provides strong evidence to support natural hybridization as an important evolutionary process in the speciation of Nepenthes. The results support an ancient circum-Indian Ocean origin for Nepenthes, indicating the disjunct species to represent relictual taxa, with a geologically recent and rapid expansion into South East Asia. A phylogenetically consistent classification of the species is proposed.