A recent study suggested that recent nuclear gene introgression between Drosophila simulans and D. mauritiana may have obscured efforts to estimate the phylogeny of the species of the D. simulans clade, which includes these two species and D. sechellia. Here, we report sequence variation of an intron of the eyeless gene in this species group. This gene should introgress freely between these species because it is not linked to any known barriers to gene exchange. We have also reevaluated levels of sequence divergence among species in this clade, noting differences between loci in regions of low recombination (as in all chromosome 4 loci) relative to other loci. Overall, none of the data analyzed were consistent with recent introgression exclusively between D. simulans and D. mauritiana.