The 1999–2000 St. Bonaventure Bonnies men's basketball team represented St. Bonaventure University during the 1999–2000 NCAA Division I men's basketball season.

The Bonnies, led by 8th-year head coach Jim Baron, played their home games at the Reilly Center and were members of the Atlantic 10 Conference.

They finished the season 21–10, 11–5 in A-10 to finish in second place.

They lost to Temple in the championship game of the A-10 Basketball tournament, but did earn an at-large bid to the 2000 NCAA tournament where they lost in the opening round to Kentucky, 85–80 in 2OT.

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