The intergenic regions between the duplicated amylase coding regions (Amy) of D. melanogaster and D. teissieri were sequenced. Their lengths in D. melanogaster and D. teissieri were 4,536 bp and 4,621 bp, respectively. Since homology between the upstream regions of the two duplicated genes was found up to 450 bp from the initiation codon of the Amy genes, the ancestral Amy coding region duplicated together with at least 450 bp of the 5'-flanking region as one unit. Comparison of the regions between the two species revealed that the level of divergence was very heterogeneous. Although the mean level of the nucleotide difference in this region was 0.107, no nucleotide substitution was found in four subregions whose sizes were more than 100 bp. Since the probability of these four subregions being completely conserved between D. melanogaster and D. teissieri was very low, these subregions were considered to have relatively important roles in evolution. Large insertions and deletions were not observed in this region but small ones were observed all over the region except for an about 1-kb subregion. This 1-kb region corresponded to an open reading frame encoding a protein which had some sequence identity with the proteins of the serine protease inhibitor superfamily (serpin). Since we could find a transcript of this gene and the synonymous substitution rate was higher than the replacement substitution rate, we suggest that this gene encodes an active serpin in Drosophila.