The couple, who came to France in the late 1980s, have been charged with complicity in violence, “having brought about the mutilation of a minor of less than 15 years old”.
They face up to 15 years in jail.
Female genital mutilation, also known as female circumcision, is traditional in about 30 African countries but illegal in France.
The couple’s two elder daughters were found to have been mutilated after one of them, then aged 14, was admitted to hospital for appendicitis in Nevers, central France.
After at first denying any knowledge of genital cutting, the father went on to mention a woman who might have practised it, while denying that he knew it was illegal in France and that he had agreed to it taking place.
The couple were placed under judicial control, a form of parole.
At the time the two younger girls had not been circumcised but they were found to have undergone the operation in 2009 when hospital staff again notified the authorities after the youngest, then aged seven, was admitted with heavy bleeding from the vagina.
Again the parents denied any knowledge and the girls refused to say what had happened.
Their defence will “explain the reason why and the cultural context”, rather than denying that the incident took place, their lawyer Guillaume Valat told the AFP news agency.
“This case is a first in so far as the parents were warned in 2005 but did it again,” lawyer Linda Weil-Curiel, acting for the Committee for the Abolition of Sexual Mutilation, said.
About 40 vaginal mutilation cases have been taken to court in France, she added.