Among the Drosophila species of the melanogaster subgroup, the island endemic D. sechellia is unique for its specialization on noni fruit (Morinda citrifolia), which is toxic to related species, making it a renown system for the genetics of detoxification and ecological and diet shift. We recently discovered a second, younger case of Morinda specialization in the same clade, involving a unique population of D. yakuba from the island of Mayotte. D. yakuba was found exclusively amongst Morinda on this island, and it shows greatly increased preference and tolerance for the fruit compared with mainland populations. Partial prezygotic isolation is also present, in that island females strongly discriminate against mainland males. Based on a population genomic analysis, these traits have evolved within the past ~30,000 years. Therefore, genetic variation may still hold signals of natural selection at causative genes, providing a major advantage of this system. Using a new FST-based statistic called Population Branch Excess (PBE), we identified notable outliers for high genetic divergence in the island population, including several loci with known detoxification genes. We tested for an association between our D. yakuba outliers and D. sechellia trait mapping intervals, finding a significant enrichment for tolerance loci but not attraction to Morinda. Thus, some of the same genes may have contributed to Morinda specialization in these two species, reflecting a shared genetic tool kit for detoxification. The existence of a young specialist population of D. yakuba will provide noteworthy opportunities to study the genetics of ecological shift, reproductive isolation, and parallel evolution.