A partial paired gene of Drosophila willistoni containing the paired box and extended homeo box was amplified by PCR and the nucleotide sequence of 1141 bp was determined. Comparison of the paired genes in D. willistoni and D. melanogaster showed that the proportions of identical nucleotide sites in the coding region and identical amino acid sites were 73.8 and 86.5%, respectively. The amino acid sites in the N-terminal region, the paired box, and the extended homeo box were 88.5, 95.3, and 98.6% identical in the two species. The rates of amino acid substitution for these regions were estimated to be 1.73 x 10(-9), 0.67 x 10(-9), and 0.19 x 10(-9)/site/year, respectively. In contrast, the connecting region between the two boxes has been highly diverged and evolved very rapidly, 18.3 x 10(-9)/site/year, suggesting almost no functional constraint in the connecting region.