This document summarizes a study that mapped 72 dinucleotide microsatellite loci from Drosophila subobscura onto its polytene chromosomes using fluorescent in situ hybridization (FISH). The distribution of microsatellites was not uniform across chromosomes, with higher density in the sex chromosome than autosomes. Homologous regions were identified in D. pseudoobscura and D. melanogaster genomes, supporting conservation of chromosomal elements among Drosophila species but also intrachromosomal rearrangements within lineages. The lack of microsatellite repeats in homologous D. melanogaster sequences suggests convergent evolution for high density in the X chromosome distal region.