ZnSe nanocrystals (NCs) were synthesized by aqueous method and were grown by microwave irradiation times (MWIRT) of 0–6 min at fixed solution pH of 11.2. Disk diffusion antibacterial property of these nanocrystals owing the mean size of ~ 2 nm, was carried out against the Gram negative bacteria of Escherichia coli and Pseudomonas aeruginosa, by considering nanoparticle loading volumes of 140 and 70 µl, showing good control over the mentioned bacteria; the maximum inhibition level at different MWIRT is devoted to Pseudomonas aeruginosa with average inhibition zone diameter of 10.10–11.58 mm for volume of 140 µl and 7.42–10.67 mm in volume of 70 µl, implying an increasing trend with increase of loading volume/ decrease of NCs size. So, these nanomaterials, which can be prepared in a simple and cost-effective manner, may be suitable as new types of bactericidal materials.