In a wireless communication system a base station apparatus and a mobile station apparatus communicate with each other. The base station sets the number of spatial multiplexing sequences (rank) of data being used by the mobile station when transmitting a PUSCH, further sets orthogonal resources used by the mobile station for the same number of reference signals as the set number of spatial multiplexing sequences which are transmitted together with the PUSCH, and transmits downlink control information indicating the number of spatial multiplexing sequences and information indicating the orthogonal resources for the reference signals. The mobile station receives the downlink control information, selects orthogonal resources to respectively apply to the reference signals, applies the selected orthogonal resources to generate the reference signals, and transmits the generated reference signals to the base station apparatus.