Abstract: Proper phylogenetic reconstruction is crucial for understanding many evolutionary phenomena. In spite of the great success of molecular phylogenetics, DNA signal still may be limited by some intrinsic constraints such as codon usage bias. The phylogenetic relationships between the five species subgroups of the Drosophila saltans group are a good example of conflicting molecular phylogenies drawn from different genes due to an ancestral substitutional shift. Here, forty morphological characters were analyzed using the same set of species used in previous molecular studies, with at least a single representative of each subgroup. The cladistic analysis was in disagreement with most of the previous hypotheses in placing the sturtevanti subgroup as an early branch, whereas the four remaining subgroups form a well supported clade that can be further subdivided into two sister clades: one containing the cordata and the elliptica subgroups, whereas the second includes the parasaltans and the saltans subgroups. The molecular evolution (codon usage bias) of the saltans group were revised in light of the present finding. The analysis highlights the important role of morphology in phylogeny reconstruction and in understanding molecular evolutionary phenomena.