Marrero graduated from American Heritage School, a private school in Plantation, Florida. As a freshman in 2010, he hit a .397 batting average with 42 runs batted in to earn a spot on the Collegiate Baseball First Team Freshman All-American squad as well as Pac-12 All-Conference honorable mention honors. He really took off in the 2011 season, in which his sterling defense led him to be named the Pac-10 Defensive Player of the Year and earned a spot on the All-Pac-10's first team, all while hitting a .313 average.
Entering 2013, Marrero is ranked as the best 11th prospect in the Red Sox minor league system. He was invited to spring training, to become the first Red Sox position player to attend the training camp spring training the season following the year he was drafted since Scott Hatteberg in 1991 and 1992. He began 2013 with the Salem Red Sox and was promoted to the AA Portland Sea Dogs after hitting .256 over 85 games.
Marrero began the 2014 season with Portland and, after hitting .291 over 68 games, he was promoted to the AAA Pawtucket Red Sox. He hit .210 over 50 games with Pawtucket. Following the 2014 season, Marrero was named the Red Sox Minor League Defensive Player of the Year.