Moringa oleifera flower extract, with trypsin inhibitor activity, is a larvicidal agent on Aedes aegypti. This work reports the isolation of trypsin inhibitor (M. oleifera flower trypsin inhibitor (MoFTI)) and its effect on A. aegypti egg hatching, viability of newly hatched larvae, survival of pupae, and growth of inhabitant bacteria from midgut of fourth-instar larvae (L4). MoFTI (K i, 2.4 μM), isolated by affinity chromatography on trypsin-agarose column, was an 18.2 kDa polypeptide on sodium dodecyl sulphate-polyacrylamide gel electrophoresis. Flower extract (at concentrations of 8.5-17.0 mg/mL) reduced egg hatchability while MoFTI (0.05-0.5 mg/mL) did not affect the hatching rate. Mortality of newly hatched larvae ranged from 3.5 to 19.1 % in the presence of the extract (4.0-17.0 mg/mL) and was also promoted by MoFTI (LC50, 0.3 mg/mL). After 72 h, larvae incubated with extract at 13.0 and 17.0 mg/mL were at stages L2 and L1, respectively, while in control they reached L3 instar. In the presence of MoFTI, at all concentrations tested, the larvae did not pass the first instar. Flower extract and MoFTI did not interfere on pupae survival. The extract and MoFTI inhibited the growth of L4 gut bacteria (minimum inhibitory concentrations of 3.47 and 0.031 mg/mL, respectively) but only the inhibitor showed bactericide effect (minimum bactericidal concentration of 1.0 mg/mL). The findings reported herein indicate that MoFTI constitutes a larvicidal principle from M. oleifera flowers against A. aegypti newly hatched larvae and is an antibacterial agent active against the microbiota from L4 gut.