In 1985, Alomar signed with the San Diego Padres at age 17, and joined the team's Class-A affiliate in Charleston.[7] The following year, playing in Reno, he won the California League batting championship with a .346 average.[7]
Alomar entered the major leagues in 1988 with the Padres, where he was an excellent fielder with speed and a solid bat. Defensively, he displayed excellent lateral range and a powerful arm, often making spectacular plays on ground balls hit deep in the hole between first and second base, and on balls hit up the middle well behind second base. He was an All-Star for the first time in 1990, as a reserve player for the National League.[7]