Employing nanomaterials and nanoparticles in the industrial and research area could reduce use of certain agrochemicals such as pesticides, and further provide a better ability to control the application and dosage of active substance to the target. Here, the use of silica nanoparticles (SiNPs) as biopesticide was applied in attempt to bring a number of benefits into potential applications of nanotechnology to pesticides; in addition, to provide a review to explain in vivo biological effects using Drosophila melanogaster fruit fly. In this study, SiNPs were used in the form of nanometer silicon dioxide (10-20 nm SiO2). The effects of exposure to SiNPs (100, 250, 500 and 1000 ppm) on larval deform, larva-to-adult viability, body size, chromosomal rearrangements, protein and isozymes expression as well as DNA content were evaluated in Drosophila flies by using morphological, cytological and biochemical analysis. All SiNPs concentrations had no toxic effect on larva-to-adult viability or body size of D. melanogaster, although the ingested SiNPs concentrations showed significantly deformation in mouth and body parts and became incorporated into organs of D. melanogaster larvae in a dose-dependent manner; compared with control. This suggests that SiNPs ingested by these insects have negligible physiological impact. On the other hand, we cannot exclude other genotoxic effects. SiNPs at the concentrations of 500 and 1000 ppm appeared to be more affective on salivary gland chromosomes than the other two concentrations. SiNPs induced specific changes in the number and intensity of total protein as well as the activity of esterase and peroxidase isozymes. Moreover, SiNPs significanty reduced DNA content in dose dependent manner. These toxic effects were closely related to the concentration used. From all the above mentioned results, the level of SiNPs could now be determined to be introduced to control the insects based on the physiological level, in addition to maintain and protect other organisms at the genetically level of these nanoparticles.