Space arms such as SSRMS and JEMRMS are designed by the concept of the macro-micro manipulator system, where the macro arm provides a long-reach capability and the micro arm performs the dexterous manipulation. One drawback however is that the macro part is subject to vibrations due to flexibility. Since the macro and micro parts are dynamically coupled, the motion of the small arm induces vibrations into the macro part hence, resulting in degradation of its positioning accuracy. To cope with this drawback, control strategies for minimization of vibration excitation and for maximization of vibration dumping have already been developed. However those strategies require an accurate model of the manipulator dynamics. If a payload with unknown parameters is being handled, the usage of the above stated strategies will lead to vibration excitation, or to inaccurate positioning of the end point. This paper presents two methods for on-line parameter identification of an unknown payload handled by JEMRMS. Both methods can be applied simultaneously while vibration suppression control is performed. The first one is vibrational motion based method, and the second one requires information about reaction forces and torques induced from the motion of the small arm. Simulation results illustrate the validity and applicability of both methods.