The club returned to the Spanish top flight under the 48-year-old's guidance last season with a second-placed finish, and they have maintained their form into the new campaign.
Seven victories in their opening 13 games in the league sees them fourth in the table, and the club have moved to secure the coach's future.
"Villarreal CF coach Marcelino Garcia Toral have agreed to the contract extension that keeps coach with the club for two seasons," a statement on the club's official website said on Thursday.
Marcelino initially signed a short-term deal at El Madrigal with an option for a further year, and will now remain at the club until 2016.
