The Japanese asteroid exploration spacecraft Hayabusa autonomously performed touchdown two times in November 2005. The autonomous guidance and navigation capability is installed aboard the spacecraft. The GNC system collects the laser altimeter, laser range finders and navigation cameras information aboard and is designed to estimate where the spacecraft is and to decide the path correction maneuvers. The programmed function includes the image processing designed to detect an artificial target marker location to approach and cancel the relative velocity. A terrain alignment maneuver is also accomplished by both altitude and attitude control. This paper presents how autonomous guidance and navigation was performed in Hayabusa mission.