The investigation of the biocompatibility of potential and commercially available dental material is a major challenge in dental science. This study demonstrates that the zebrafish model is a novel in vivo model for investigating the biocompatibility of dental materials. Two commercially available dental materials, mineral trioxide aggregate (MTA) and Biodentine, were assessed for their biocompatibility. The biocompatibility analysis was performed in embryonic zebrafish with the help of standard toxicity assays measuring essential parameters such as survivability and hatching. The mechanistic and comparative analysis of toxicity was performed by oxidative stress analysis by measuring ROS induction and apoptosis in zebrafish exposed to dental materials at different concentrations. The molecular investigation at the protein level was done by a computational approach using in silico molecular docking and pathway analysis. The toxicity analysis showed a significant reduction in hatching and survivability rates along with morphological malformations with an increase in the concentration of exposed materials. ROS and apoptosis assay results revealed a greater biocompatibility of Biodentine as compared to that of MTA which was concentration-dependent. In silico analysis showed the significant role of the tricalcium silicate-protein ( Sod1, tp53, RUNX2B) interaction in an exhibition of toxicity. The study provides a new vision and standard in dental material sciences for assessing the biocompatibility of potential novel and commercially available dental materials.