Surgical robotic systems and navigation systems employ a robotic arm including a plurality of links. A link tracker assembly is located on the surface of one or more of the links to enable the link to be tracked by a localizer. The link tracker assemblies can utilize a plurality of tracker elements that can be removably coupled to the link. A photosensor assembly is located on the surface of one or more of the links to receive signals from the localizer for controlling the link tracker assembly. The robotic arm can be coupled to a base and the systems can be used in collaboration with a base tracker that is coupled to the base. The robotic arm can also include a mounting interface for receiving an end effector and the systems can be used in collaboration with an end effector tracker that is coupled to the end effector.