This is the first extensive molecular phylogeny for any group of Solanum in Australia. A total of 64 specimens representing 29 taxa were sampled, including 18 endemic Australian members of subgenus Leptostemonum (the “spiny solanums”) section Melongena sensu Symon. Data from the rDNA ITS region were analyzed using parsimony, maximum likelihood, and Bayesian methods to test the hypothesis that the dioecious and andromonoecious Australian species of section Melongena constitute a monophyletic group. Analyses showed support for the recognition of five clades among the Australian species of the section, but little support for the monophyly of the section itself. Australian dioecious Solanum species form two distinct clades and a number of enigmatic and previously unplaced dioecious taxa are here placed within a single clade. Three groups of andromonoecious species are also each monophyletic and are nested in a polytomy with three clusters of species from outside section Melongena. Furthermore, the phylogeny indicates that dioecy has evolved either once or twice in Australian Solanum, possibly from andromonoecious ancestry.