In 1996 he became Chancellor of the UCSD campus, then in 2003 was chosen to be the 18th President of the University of California system.
Dynes remains active in his research and heads a modest sized low temperature physics laboratory at Berkeley.
After five tumultuous years as President of UC, filled with compensation scandals, the suicide of UCSC Chancellor Denice Denton and other challenges,[2][3][4] on August 13, 2007, Dynes announced he would resign his position as the President of the University of California to return to his teaching position and spend time with his new wife, Ann Parode.
In November 2008, Dynes' close aide and his UC Associate President Linda Morris Williams was awarded a controversial pay out[5][6] and re-hired as an Associate Chancellor at University of California, Berkeley by Chancellor Robert Birgeneau.
He married a former UCSD legal counsel and UC Associate of the President, Ann Parode,[10] in March 2007.