Rubiales also resigned his position as Vice President of UEFA's Executive Committee.
Luis Rubiales has resigned as President of the Spanish Football Federation.
It comes following calls for him to step down after he kissed Jenni Hermoso in the aftermath of Spain's World Cup triumph last month.
Rubiales has also resigned his position as Vice President of UEFA's Executive Committee.
Spain forward Jenni Hermoso filed a criminal complaint last week, which led to prosecutors filing a case with Spain's top court against Rubiales.
He faces charges of sexual assault and coercion for his conduct after last month's Women's World Cup final, which Spain won 1-0 against England.
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