The former Real Madrid stopper moves to Villarreal on a season-long loan.
The deal includes a permanent option, confirmed Villarreal on Wednesday evening.
Marin joins the Yellow Submarine after managing just six appearances in Napoli's title-winning season last term.
Villarreal will pay initial €1m loan fee for Marin, a Spain U21 international. The 23 year-old moves to Napoli a year ago from Real Madrid for a fee of €12m.
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Napoli
Villarreal
Rafa Marín