Two implant types of hydroxyapatite (HA) currently are available for dental implants: dense HA-cemented titanium (Ti) and HA-coated. It has been shown in previous reports that there are differences in the chemical and mechanical stabilities between the dense HA and HA coated. The differences are thought to be due to structural differences between the two ceramic types. The aim of this study was to investigate the differences in microstructural characteristics of currently available dense HA and HA coated implants before implantation and at periods of 3 weeks and 10 months after implantation in canine bone. X-ray diffractometry, infrared analysis, transmission electron microscopy, and energy dispersive X-ray analysis were used. The dense HA is composed of crystal grains, with a well crystallized structure of HA, closely bound to each other and approximately 0.4-0.6 micron in size. Implantation did not change the original sintered structure of the dense HA. The HA coating was composed of an amorphous phase with a Ca/P ratio of 1.46 and a crystal phase consisting of oxyhydroxyapatite, tricalcium phosphate, tetracalcium phosphate, and CaO, with a Ca/P ratio of 1.57. In the amorphous phase, compared to other portions in the amorphous phase, there were some layers with lower atomic density and with no significant difference in Ca/P ratio. After implantation, the crystallization of super fine crystals of approximately 4-5 nm in thickness occurred in the amorphous phase, and with time it progressed and spread from the surface to the deeper portion of the HA coating. A Ca/P ratio of 1.58 in the crystallized portion was close to the ratio (1.60) in the dense HA, suggesting that the super fine crystals were HA. This crystallization cannot significantly decrease the solubility of the amorphous phase portion and poses risks of stress accumulation within the coating and a decrease of binding strength between the HA coating and the substrate.