The fruit fly Drosophila persimilis is a member of the obscura group of the subgenus Sophophora and one of 12 fruit fly species whose genomes were sequenced for use in comparative genomics studies. The whole genome sequences combined with previous information on the phylogenetic relationship between these species provides a resource to aid in studies of molecular evolution, gene function and comparative annotation across the entire Drosophila genus. Twenty fruit fly species have been approved for construction of BAC libraries, which will further assist in expanding our knowledge of gene homologies and pathway discovery.