The Drosophila nasuta subgroup of the immigrans species group is widely distributed throughout the South-East Asian region, consisting of morphologically similar species with varying degrees of reproductive isolation. Here, I report nucleotide variability data for five X-linked and two mtDNA loci in eight taxa from the nasuta subgroup, with deeper sampling from D. albomicans and its sister species D. nasuta. Phylogenetic relationships among these species vary among different genomic regions, and levels of genetic differentiation suggest that this species group diversified only about one million years ago. D. albomicans and D. nasuta share nucleotide polymorphisms and are distinguished by relatively few fixed differences. Patterns of genetic differentiation between this species pair are compatible with a simple isolation model with no gene flow. Nucleotide variability levels of species in the nasuta group are comparable to those in members of the melanogaster and pseudoobscura species groups, indicating effective population sizes on the order of several million. Population genetic analyses reveal that summaries of the frequency distribution of neutral polymorphisms in both D. albomicans and D. nasuta generally fit the assumptions of the standard neutral model. D. albomicans is of particular interest for evolutionary studies because of its recently formed neo-sex chromosomes, and our phylogenetic and population genetic analyses suggest that it might be an ideal model to study the very early stages of Y chromosome evolution.