In one embodiment of the invention, a method for a robotic system is disclosed to track one or more robotic instruments. The method includes generating kinematics information for the robotic instrument within a field of view of a camera; capturing image information in the field of view of the camera; and adaptively fusing the kinematics information and the image information together to determine pose information of the robotic instrument. Additionally disclosed is a robotic medical system with a tool tracking sub-system. The tool tracking sub-system receives raw kinematics information and video image information of the robotic instrument to generate corrected kinematics information for the robotic instrument by adaptively fusing the raw kinematics information and the video image information together.