Magnetic hydroxyapatite/chitosan nanocomposites were prepared via in situ hybridization strategy in the ambient condition. Magnetic hydroxyapatite/chitosan nanocomposites were investigated by XRD, SQUID and TEM. XRD results indicated that the inorganic phases dispersed in chitosan matrix were composed of magnetite and hydroxyapatite. The magnetic hydroxyapatite/chitosan shown the behavior of superparamagnetism determined by SQUID, which indicated the size of magnetite crystal were less than 30nm. The inorganic nanoparticles with size of 30-50nm were dispersed chitosan matrix homogeneously. In situ hybridization strategy provided a simple and efficient route to synthesize the magnetic chitosan/hydroxyapatite nanocomposites in the mild condition. The most important of in situ hybridization is that the processes of precipitation of chitosan, synthesis of magnetite and hydroxyapatite, and compositing between three components were completed in single step.