Mr Rubiales was forced to resign, but has denied any wrongdoing.
According to a court document seen by Reuters, prosecutor Marta Durantez charged Mr Rubiales with one count of sexual assault and one of coercion for his alleged actions in the aftermath of the kiss. The charges carry prison terms of one year and 18 months respectively.
Ms Durantez also accused the former coach of the women's national team, Jorge Vilda, the team's current sporting director, Albert Luque, and the federation's head of marketing, Ruben Rivera, of coercing Ms Hermoso into saying the kiss was consensual.
The indictment said they harassed her through "constant and repeated acts of pressure", including through her friends and family.
All three denied wrongdoing when they appeared before the court. Each could face up to 18 months in jail if convicted.