Undrafted, Mowers played collegiate hockey at the University of New Hampshire. Mowers played for the Whitesboro Warriors high schoolhockey team in Whitestown, New York, graduating from Whitesboro High School. After his senior year, in which he was named to the East First All-American Team, Mowers was signed as a free agent by the Nashville Predators on August 1, 1998. Mowers made his NHL debut in the 1998–99 season, his first pro season, with the Predators. Mowers played in 30 games with the Preds and split the season with their affiliate, the Milwaukee Admirals. Mowers spent the next three seasons with the Predators. On August 6, 2002, Mowers signed a contract with the Detroit Red Wings. Mowers was assigned to the Grand Rapids Griffins for the 2002–03 season and scored 81 points in 78 games, to earn a spot on the AHL All-Star Second Team. In the following 2003–04 season, Mowers started the year with the Griffins before he was recalled by the Red Wings on November 19, 2003. Mowers impressed in a checking line role and established a regular place on the team. Mowers suffered a foot injury towards the end of the season and missed the playoffs. During the 2004 NHL Lockout, Mowers played with the Malmö Redhawks of the SEL and Swiss team Fribourg-Gottéron. Mowers returned to the Red Wings for the 2005–06 season and was used as a reserve forward, playing in 46 games. On July 6, 2006, Mowers signed a two-year contract with the Boston Bruins, following former Red Wings head coachDave Lewis. Mowers played in a career-high 78 games in the 2006–07 season and posted 17 points. Prior to the 2007–08 season, on September 24, 2007, Mowers was traded by the Bruins to the Anaheim Ducks for Brett Skinner and Nathan Saunders. Mark played in 17 games with the Ducks and accepted a loan to SC Bern of the NLA for the remainder of the season on November 30. Mowers returned to his former Swiss team, Fribourg-Gottéron, for the 2008–09 season and played three more professional seasons in the NLA before ending his playing career after the 2010–11 season.
Post-retirement
Mowers first foray was doing intermission broadcasts during Boston Bruins games on New England Sports Network. On August 17, 2012, Mowers was named pro scout of the NHL's Eastern Conference for the Montreal Canadiens. Mowers remained a scout with the Canadiens for the following 5 seasons before leaving to accept the same role with the Buffalo Sabres for the 2017–18 season. Mowers is now with the Minnesota Wild as of July 2019 as a pro scout.