This paper proposes a bilateral control method focusing on the stability and force estimation accuracy for a pair of two-degrees of freedom(DOF) manipulators which have different structures. Bilateral control is a method that controls position and force bidirectionally between master and slave. By using this method, operators can get haptic sensation from the remote environment during teleoperation. In the practical situation, the desired structure would be different between master and slave depending on the task or environment. Therefore, it is important to consider the bilateral control between different structural manipulators. In this case, bilateral control needs to be realized in the workspace, which is the set of points that can be reached by the end-effector. In the method using Workspace Observer(WOB), the nominal value of the equivalent mass matrix is set to prevent it from diverging when the manipulator is around singular configurations. However, an error occurs between the nominal and true equivalent mass matrix, and this error deteriorates the stability of the system. In addition, it deteriorates the accuracy of the force estimation since Reaction Force Observer(RFOB) estimates external force including this error. To overcome this problem, the joint space based bilateral control for the different structural manipulators is proposed. Simulations are conducted to validate the proposed method.