Nanobacteria is a tiny structure with size varying 80 to 500nm, commonly occurring in clusters and producing a biofilm which contains carbonate or hydroxyl apatite. In this study, the bioactive synthetic hydrogel materials were prepared with polyethylene glycol diacrylate (PEGDA) and 2-hydroxyethyl mathacrylate (HEMA) by UV photo-polymerization. Bone marrow mesenchymal stem cells (BMSCs) were seeded onto hydrogel surface for five days. The BMSCs cell adhesion on hydrogels was confirmed by SEM to evaluate the biocompatibility of the materials. It was found groups of nanoparticles on the hydrogel surface and the particles were analyzed by SEM. The particles were analyzed for its inorganic chemical constituents using energy dispersive X-ray microanalysis (EDS). The predominant components were found to be calcium (24.40%) and phosphorus (13.98%). The most likely source of cell culture contamination by such organisms is bovine serum albumin (BSA) used as supplement in culture media. Nanobacteria in BSA may be the important factor which accelerated hydroxyapatite crystal growth on hydrogels. It is important to study the biomineralization in biological system and has potential application in biomaterials science and biotechnology.