The study aimed to assess the antimicrobial activity of Azidirachta indica mediated selenium nanoparticles (SeNPs) against oral pathogens and investigate their embryotoxic effects using zebrafish embryos. The concentrations of SeNPs tested were 25 μg/mL, 50 μg/mL, and 100 μg/mL, with comparisons made to a standard antimicrobial agent. The green synthesized SeNPs were characterized using UV-Visible spectrophotometer. The antimicrobial activity was evaluated against oral pathogens including C. albicans, E. coli, S. mutans, and Lactobacillus sp. The hatching rates and viability of zebrafish embryos were assessed at different concentrations of SeNPs. The green synthesized SeNPs showed its absorption peak at 360nm. SeNPs exhibited varying degrees of antimicrobial activity against the tested pathogens, with the highest inhibition observed at 100 μg/mL for C. albicans, E. coli, and S. mutans. The hatching and viability rates of zebrafish embryos decreased with increasing concentrations of SeNPs, indicating a dose-dependent action. The results suggest that A. indica mediated SeNPs possess significant antimicrobial activity against oral pathogens, with potential as an antimicrobial agent. However, the embryotoxicity study revealed a concentration dependent impact on hatching success and viability of zebrafish embryos at higher concentrations of SeNPs. A. indica mediated SeNPs show promise as antimicrobial agents against oral pathogens, but their embryotoxic effects warrant further investigation to determine safe concentrations for potential applications.