A phylogenetic approach based on morphological characters is the only alternative applicable in cases where molecular data are unavailable. During a taxonomic inventory of Drosophilidae in 12 localities of Ecuador (South America), we discovered a new species of cactophilic spotted-thorax Drosophila Fallen that here we formally describe as Drosophila machalilla Acurio 2013. To classify this new species, we analyzed the terminalia of male and female adults, finding similarities with flies of two neotropical spotted-thorax species groups of Drosophila, namely rep leta and peruensis. Flies or DNA sequence data are unavailable for the latter species group, hindering a molecular approach. Thus, to accurately classify the new species, we carried out a maximum parsimony cladistic analysis using 52 morphological characters from nine representative taxa of virilis, willistoni, repleta, and peruensis species groups. The results indicate that D. machalilla sp. nov. belongs neither to the repleta group nor to the peruensis group and suggest that a new species group should be erected to house D. machalilla and Drosophila atalaia Vilela & Sene (1982, previously considered a member of the peruensis species group).