Objective(s): The production of nano-hydroxyapatite by two encapsulated bacterial strains was the goal of current research.Materials and methods: Serratia marcscens ATCC 14756 and Pseudomonas aeruginosa PTCC 1570 were used by two methods including encapsulated form in 2% (w/v) alginate sodium powder and inoculated form (10%) in nutrient broth medium containing alginate sodium blank beads. In both cases alginate beads transferred to calcium and phosphorus precursors mineral medium for 48 h and were incubated at 32-35oC for 14 days. To obtain hydroxyapatite powder, alginate beads were dried at 60oC and rubbed. Sol-gel as chemical method was used for comparing with microbial analysis. The nature of produced powders was evaluated in each step by XRD, FTIR and scanning electron microscopy.Results: The results showed that the yield rate of sol-gel method was 18.3% and it was much more than encapsulated method (3.032 and 3.203 w/w dried alginate bead). The size of the particles in microbial method were smaller (8-68 nm cylindrical particles and 12-55 and 15-37 nm spherical particles) than chemical method (350-880 nm of cylindrical and 34- 67 nm of spherical particles).Conclusion: Nanoparticle sizes and distribution of microbial nano-hydroxyapatite powder samples shows that it has excellent physical properties similar to natural bone and may be to produce dense and porous bioactive bone implants with desired properties.