The high concentration of the pesticide residues existing in vegetation, crops, and various edible products and the prolonged exposure to them, can harm human life and contribute to the disappearance of honey bees, several avian and animal species. The honey bees (Apis mellifera), efficient pollinators in addition to honey producers, are also considered important non-target test species for terrestrial toxicity assessment of chemicals. In this context, using thiacloprid and acetamiprid as queries, we performed a 3D similarity search to select new potential products with less harmful effects against bees. For similarity search, a small dataset of 302 compounds with pesticide activity, compiled from literature, was used. The first 10 compounds were selected and structurally analyzed according to the TanimotoCombo metrics, and compared with each of these two queries known to be effective, easily metabolized, and less toxic for bees. This approach came as a forward step in the research of pesticide ecotoxicological risk assessment, for the evaluation of their potential impact on the pollinator insects and the environment.