The Marlins also announced the hiring of Rob Leary as bench coach Friday.
Hernandez spent the past two years as an assistant coach at the University of South Florida. He was pitching coach for the Detroit Tigers in 2006-08 and for Tampa Bay in 2004-05, and pitched in the minor leagues from 1979-83.
Leary was minor league field coordinator for the Cleveland Indians in 2012. He spent the 2010 and '11 seasons as the Red Sox's major league coaching staff assistant.