Judge Fernando Andreu also indicted them for the murder of nine Spanish citizens, including six missionaries.
He said he had evidence implicating Rwanda’s current President Paul Kagame, who has immunity from prosecution.
Under Spanish law, a court can prosecute human rights crimes even if the alleged offences took place abroad.
During a 100-day period in 1994, an estimated 800,000 Rwandans were killed, mainly ethnic Tutsis at the hands of radical Hutus.
The genocide came to an end when Tutsi-led rebels under Paul Kagame took control.
But the judge said that, after taking power, the army under Mr Kagame carried out mass killings of Hutus in Rwanda and in refugee camps in what was then neighbouring Zaire.
The indicted members military are also accused of crimes against humanity, genocide and terrorism.
Previous attempts by Spanish judges to open human rights cases against foreign figures have largely failed.
In 1998, former Chilean president Augusto Pinochet was indicted while in London but not extradited.