Camel melon (Citrullus lanatus), colocynth (Citrullus colocynthis) and prickly paddy melon (Cucumis myriocarpus) are summer-growing invasive weeds distributed throughout Australia. We used DNA-sequence information from samples collected across Australia and morphological data from glasshouse-grown plants to determine diagnostic features of these species, and to determine the infraspecific identity of Australian Citrullus lanatus and Cucumis myriocarpus. All species possessed distinct genotypes and haplotypes at nuclear G3pdh and chloroplast ycf6–psbM gene regions and could be easily identified on the basis of molecular phylogenetic analysis. A combination of vegetative, floral, fruit and seed characters also allowed for species identification at all developmental stages. On the basis of our morphological and molecular analyses, Australian camel melon and prickly paddy melon populations were identified as Citrullus lanatus var. citroides and Cucumis myriocarpus subsp. myriocarpus respectively.