Florent Lemacon, left, was killed during the rescue effort
Three suspected Somali pirates have been charged with hijacking and false imprisonment, French prosecutors say.
The three were captured by French commandos in a hostage rescue operation in the Indian Ocean on 10 April and brought to France to face trial.
Two pirates and the skipper of the yacht Tanit were killed and four hostages freed in the operation.
It is not yet known if the Tanit's captain was killed by his captors or hit by a stray French shot.
The three Somalis captured on the Tanit, aged 23-27, were taken to the town of Rennes for questioning.
They face a life sentence in prison if convicted of the charges.
A post mortem examination has revealed that the captain, Florent Lemacon, 28, died of a gunshot wound to the head.
As no bullet fragment was found it has not yet been determined if the shot was from a French weapon or a hijacker's gun, officials said.
Mr Lemacon's three-year-old son, his wife and two other people aboard the 12.5m (41ft) boat were rescued unharmed after being held by pirates for five days off the coast of Somalia.
French commandos stormed the boat after negotiations with the pirates to free the hostages broke down.
The Tanit was reported to be sailing down to Zanzibar, off the coast of Tanzania, despite warnings not to sail through the area.
Despite patrols by the French, US and other navies in the Gulf of Aden and the Indian Ocean off Somalia, there has been a surge of pirate attacks in what is one of the world's busiest sea lanes.
Twelve other suspected pirates captured in two other attacks on French vessels are being held in France.
Another 11 suspected pirates arrested on Wednesday by the French navy are being taken to the Kenyan port of Mombasa to face trial there.
Kenya has already prosecuted pirates as part of an international agreement.
On Friday, US officials said a pirate suspect arrested in the rescue of an American merchant ship captain would be taken to New York for trial.
He was captured after three other pirates were killed by US navy snipers during the rescue of the captain of the Maersk Alabama on Sunday.
Pirates have vowed to avenge the deaths of those killed in the rescue operations.