The national team's then sporting director Fernando Hierro stepped in to replace him and led Spain to the last 16 where they lost to hosts Russian Federation on penalties, before stepping down after the tournament.
Spain crashed out of the World Cup to Russian Federation at the last-16 stage after losing a penalty shoot-out.
Hierro, 50, has made a decision to "seek new horizons", according to the Spanish football federation (RFEF).
Rafa Benitez was linked with the Spanish national team job when Julen Lopetegui was sacked just before the World Cup kicked off.
Of the starting XI against Russian Federation, only Marco Asensio will be under 30 when the next World Cup comes around.
But now Spain have turned to Luis Enrique to guide the national team ahead of the 2020 European Championship.
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The former Barcelona manager has signed a two-year contract to take charge of his country.
Luis Enrique has played for both Real Madrid and Barcelona, as well as managing Celta Vigo, Roma, and winning the Champions League with Barcelona in 2014/15.
"Luis Enrique comes with his staff, but he will talk about that next week".
Enrique has been out of management since leaving the Nou Camp last June.
Andres Iniesta, the former Barcelona great who scored the winning goal in the 2010 World Cup final, retired from the global team after the defeat to Russian Federation.
Molina, 47, a former goalkeeper with Atletico Madrid, Deportivo La Coruna and Villarreal, earned nine Spain caps as a player.