Understanding incipient sexual isolation and speciation is an important pursuit in evolutionary biology. The fruit fly Drosophila melanogaster is a useful model to address questions about the early stages of sexual isolation occurring within widespread species. This species exhibits sexual isolation between cosmopolitan and African flies, especially from Zimbabwe populations. In addition, we have recently described another example of partial sexual isolation between some US and Caribbean populations. This and other phenotypic data suggest that Caribbean flies might be segregating African traits. In the present work we study the geographical variation at the pheromone locus desaturase-2, as well as morphology and courtship behavior across the US–Caribbean region. We find that US and Caribbean populations show sharp geographical clines in all traits and demonstrate that Caribbean traits are more similar to those of Africa than to US populations. Further, African traits in the Caribbean are associated with sexual isolation and best explain variation in sexual isolation when all traits are considered together. These results imply that Caribbean mating preferences are likely to be based on African traits and that even at such early stages of sexual isolation, individuals may already cue in on several traits simultaneously during mate choice.