Mutation of the Drosophila melanogaster mei-9 gene causes enhanced mutagen sensitivity, DNA excision repair incision deficiency, germ line hypermutability, mitotic chromosome breakage and instability, and, in females, increased levels of meiotic non-disjunction and decreased levels of meiotic recombination. This paper reports on the utilization of a positional mapping strategy combined with a differential expression assay to clone the mei-9 gene. We report that mei-9 is homologous to the yeast repair gene, RAD1, and demonstrate that the mei-9 gene transcript is absent in the mei-9AT3 mutant.