The 2006 NCAA Division III men's basketball tournament was the 32nd annual single-elimination tournament to determine the national champions of National Collegiate Athletic Association (NCAA) men's Division III collegiate basketball in the United States.

The field contained sixty-four teams, and each program was allocated to one of four sectionals.

All sectional games were played on campus sites, while the national semifinals, third-place final, and championship finals were contested at the Salem Civic Center in Salem, Virginia.

[1] Virginia Wesleyan defeated Wittenberg, 59–56, in the championship, clinching their first national title.

The Marlins (30–3) were coached by David Macedo.