The aim of the present study was to evaluate the diverse potential biological activity of partially purified crude extract (PPCEBS) of marine Bacillus subtilis NMK17 associated with marine sponge Clathria frondifera. Symbionts were isolated from a marine sponge, only the potentialstrain which exhibited apoptosis was sequenced using 16SrRNA and extract of the active strain was subjected to purification using HPLC. The potential pro-apoptotic role of PPCEBS was investigated in MCF-7 human breast cancer cell line for cytotoxicity by MTT assay, which showed dose-dependent cytotoxicity on 24h of exposure. The apoptotic findings demonstrated that PPCEBS significantly induces apoptosis, which was characterised by apoptotic morphological changes. Further, an increased expression of the Caspase 3 and Bax whereas decreased Bcl-2 was confirmed by immunofluorescence and western blotting analysis in MCF-7 cell line, which revealed that PPCEBS has potentapoptosis-inducing property. Added to the desirable apoptotic activity, PPCEBS exhibited excellent antibacterial and antioxidant activities too. The pharmacological effect of the marine sponge-associated bacteria from Gulf of Mannar India needs further attention in discovering new bioactive compounds. Our results suggested that the compounds present in the PPCEBS in marine bacterial B. subtilis NMK17 could be candidates for developing an apoptosis-specific drug with minimal toxicity. This study indicated that marine sponge-associated bacteria could be a good source to find thecytotoxic metabolites which would induce apoptosis and cause cancer cell death. Also, this study explores that marine natural products as a potential source of pharmaceuticals.