This paper proposes an antenna selection algorithm for Mars Exploration Rover (MER), where MER can autonomously select which antenna to use between X-band direct-to-Earth (DTE) and UHF for communication according to its constrains and limitation to effectively use their resources and thereby increase data return. When MER selects a path for communication, it simultaneously selects an antenna for transmission of data to earth. In our algorithm, we have defined a cost function for each possible path based on three parameters namely power required by the rover to transmit in that path, average delay, and error rate. A weighting is given to each parameter in the function based upon application quality of service (QoS) requirement. The algorithm has low computational complexity and provides optimum performance. This proposed algorithm would make MER more autonomous in terms of communication system. We have presented simulation results and analysis