Hydroxyapatite (HA) is a well known candidate for many applications in dentistry and medicine such as bone replacement and regeneration and coatings for medical implants. Nano-crystalline HA exhibits improved mechanical properties and biocompatibility. To optimize the benefits of nano-sized precursors, the particles must be of a uniform shape and size and have minimum degree of agglomeration. The aim of this study was to synthesize of nano-crystalline HA via the biomineralization route. For this purpose, an Iranian strain of Serratia (Serratia marcescens PTCC 1187) was utilized for the synthesis of nano-crystalline HA. The strain was cultivated. Then the pellet of S. marcescens PTCC 1187 was separated and exposed to Glycerol 2-phosphate and Calcium chloride. After 14 days of incubation at 37oC, the white precipitated material was separated. After drying and calcination at 600oC the powder was characterized using scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray diffraction (XRD) and fourier transform infrared spectroscopy (FTIR) techniques. The results showed that nano-structured HA powder was synthesized and the crystallinity of the powder was relatively high according to the standard. The particles of the powder were single crystal with the size of 25-30 nm. Moreover, the shape and size of the particles were relatively uniform and the agglomeration was lower comparing to the conventional methods. This powder could be used in the regeneration of bone defects, fabrication of medical, dental implants and also as a vector for pharmaceuticals and biological materials such as the genes.