Morse was acquired by the Mariners along with Miguel Olivo and Jeremy Reed for Freddy Garcia and Ben Davis on June 27, 2004. Beginning the 2005 season with the Triple-A Tacoma Rainiers, he made his major league debut on May 31, 2005. Although Morse made it to the big leagues as a shortstop, with the arrival of Yuniesky Betancourt, Morse began to develop as a utility player, having spent time at first base and left field. In 2005, he was suspended for 10 days for using performance-enhancing drugs.