1. 1. Tissue-specific α-amylase expression in midguts of axenically reared third-instar larvae of Drosophila melanogaster has been investigated on high and low protein diets with varying starch or maltose levels. 2. 2. Strains with different structural Amy variants, Amy 1 and Amy 4,6 are compared. 3. 3. On low protein food medium without starch or with low starch levels α-amylase is produced in both anterior and posterior midgut regions (AMG and PMG) of Amy 4,6 larvae, while with maltose, high starch or high protein levels α-amylase expression in the AMG disappeared. 4. 4. In contrast, under these different food conditions, Amy 1 larvae did not show changes in their α-amylase midgut pattern, which was restricted to a small region of the PMG. 5. 5. Both dietary and genetic differences can influence the tissue-specific expression of α-amylase in the larval midgut of D. melanogaster. 6. 6. The implications of these findings for characterization and identification of regulatory gene variants in Drosophila are discussed.