Mitochondrial respiratory complexes in insects are involved in diverse physiological processes including energy production. Specific and potent inhibitors of complex I, III and IV are described and has allowed in determining the importance of these enzymes in the physiological processes. However, there seems a paucity of information regarding potential inhibitors of complex II of insect mitochondria. In this study we demonstrate the toxicity of acetone fraction (ASF) of Annona squamosa seed extract to Musca domestica and its mitochondrial complexes. Effectiveness of ASF as oral bait and contact poison was also evaluated. Inhibition of Complex II in treated flies has been related to its lethargic nature. Energy inhibition study of ASF further confirmed reduction in ATP.