The present study aimed in the investigation of anticancer potential of silver nanoparticles (AgNPs) from endophytic bacterium Cupriavidus metallidurans (Cm-AgNPs) and Pantoea anthophila (Pa-AgNPs) of W. indica reported in our earlier studies, against human oral epidermoid carcinoma (KB 3–1) and COLON 26 cell lines. The cytotoxicity response was assessed by 3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide (MTT). Measurement of intracellular reactive oxygen species (ROS), mitochondrial membrane potential (ɅΨm) and apoptotic morphological changes were studied in KB 3–1 cell line. Both the endophytes were found to produce periplasmic nitrate reductase (PNR) that converts the ionic silver into stable nano silver. Hence the structure and function of PNR was determined by computationl tools and evolutionary relationships were constructed using Clustal Omega. The inhibitive properties of AgNP against selected cancer targets were analyzed by molecular docking tool Autodock 4.0. KB 3–1 cell line showed good anticancer response than COLON 26 cell lines. On comparison of AgNPs, Cm-AgNPs exhibited higher cytotoxicity with increased intracellular ROS levels, altered ɅΨm and apoptotic cell death than Pa-AgNPs. The three-dimensional structure of the PNR was modeled by Swiss model and validated using PROCHECK and PROVES. Docking study showed that the AgNP bound exactly in the inhibition site or in their close proximity that may enable the modulation of proteins. Thus the study provides an insight on the anticancer activity of AgNPs fabricated from endophytic extract.