Castro, a Hanford native who has led Fresno State for the last seven years, will replace Chancellor Timothy White to oversee the CSU.
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He is the first Mexican-American to become chancellor for the university system, which has 23 campuses across the state, including Fresno State.
"I am truly grateful for and excited about this unique and wonderful opportunity, and I look forward to working with the talented faculty, staff and presidents of the 23 campuses as well the Board of Trustees and executives and staff at the Chancellor's Office to further increase achievement for our 482,000 students," Castro said in a press release.
Before becoming president of Fresno State, Castro previously served the University of California (UC) in several roles, including the Vice Chancellor of Student Academic Affairs and as a professor of Family and Community Medicine at UC San Francisco.
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He attended UC Berkeley, where he received his Bachelor's and Master's degrees in political science and then later obtained his Ph.D. from Stanford University.
It wasn't immediately clear who would replace Castro as Fresno State's university president.