Viviparity has evolved from oviparity in many vertebrate lineages, and species that contain both oviparous and viviparous populations offer the best opportunity for a detailed examination of the processes involved in this major life-history transition. However, although several such species have been reported, none have been the subject of detailed phylogenetic analyses. We examine such a case within the Australian scincid lizard bougainvillii. Data were obtained by sequencing a 314-bp segment of mitochondrial cytochrome b from 32 individuals from 17 populations of L. bougainvillii and two morphologically similar congeneric species (L. dorsalis L. microtus). Sequences were aligned and analyzed using parsimony and distance methods. The resultant matriarchal phylogeny resolved the populations of L. bougainvillii into three major groups: a population from NSW; a group predominantly from Eyre Peninsula; and a less well-defined group from the central part of the species range. The NSW and Eyre Peninsula groups are oviparous and are quite divergent from other L. bougainvillii populations and from each other. The central group contains both viviparous and oviparous populations, and seem to represent a more recent radiation within the species. Our results indicate that viviparity has evolved at least twice within the genus Lerista, because the viviparous L. microtus is not closely related to viviparous populations of L. bougainvillii. The lack of phylogenetic separation of mtDNAs from viviparous and oviparous populations within L. bougainvillii relative to strong geographic structure within the latter indicates that populations with different reproductive modes are indeed conspecific. Lerista bougainvillii is thus the first vertebrate species for which intraspecific bimodality in reproductive mode can be claimed with any certainty.