The 60-year-old Asturian departs having overseen 298 matches across his two spells — more than any other manager in the club's history — winning 145 of them, also a record. He first joined the Yellow Submarine in 2013 and led them into the top flight before leaving in 2016.
He returned in 2023 and this season produced what could end as Villarreal's finest La Liga campaign, with the club sitting third with four games remaining, five points clear of Atlético de Madrid in fourth.
The breakdown came after contract extension talks stalled. Villarreal offered Marcelino a one-year renewal in January, but he sought a longer-term commitment that would allow him to continue building the project.
The club and the coach have also been at odds over a series of other issues — their Champions League catastrophe, in which they won just one of nine games in the league phase, Marcelino's reluctance to use academy players, his demands on recruitment and what multiple reports have described as a deteriorating relationship with the dressing room.
In a statement, Villarreal paid tribute to his contribution.
"Villarreal CF would like to publicly thank Marcelino and his coaching staff for their professionalism, commitment and work from day one, as well as their daily involvement and contribution to sporting development during the seven seasons in which he has been in charge. Thank you, from the bottom of our hearts, Marce. Thank you for everything you have given to this club and these fans. We wish you all the best in your future sporting endeavours."
Rayo Vallecano manager Íñigo Pérez, who has guided Rayo to the Conference League semi-finals in his first European campaign, has already reached a verbal agreement to take charge next season — though the deal is yet to be formally signed. Villarreal will hold a tribute to Marcelino at their final home fixture against Atletico Madrid, which will double as the club's Champions League celebration with supporters.