The spokesman for the banned Basque nationalist party Batasuna has been charged with belonging to the armed separatist group Eta.
Arnaldo Otegi had to put up 400,000 euros bail money
A national court judge indicted Arnaldo Otegi, who was arrested last week as part of an investigation into Eta.
Mr Otegi, who has been a member of the Basque regional parliament, was let out on bail of 400,000 euros (£275,266).
His former Batasuna colleague Jon Salaberria faces similar charges but absconded before the earlier hearing.
Mr Otegi's arrest prompted condemnation in the Basque region - especially as it came a week after the Spanish parliament backed a plan to allow peace talks with Eta if they laid down their arms.
The Basque separatist newspaper, Gara, blamed Spanish Prime Minister Jose Luis Rodriguez Zapatero for what it called a blow to the peace process.
The arrest came hours after a car bomb, claimed by Eta, injured five people in Madrid.
The prosecution says there is evidence that Mr Otegi and Mr Salaberria have acted as "delegates of Eta" or as links to the organisation.
Mr Otegi has previously spent four years in jail for kidnapping. The Batasuna party was banned in 2003 on grounds that it was part of Eta, but Mr Otegi kept his seat in the Basque regional parliament after the party changed its name.
He lost his MP's immunity from prosecution earlier this year when Batasuna candidates were barred from standing in April's regional elections.
Batasuna has denied being the political wing for Eta but has refused to condemn attacks by the group.
Last year, Mr Otegi called for peaceful dialogue between all sides to end decades of armed conflict, but he stopped short of making an explicit call for an Eta ceasefire.
He is due to appear before magistrates on 8 June. An international arrest warrant is out for Mr Salaberria.
Eta's campaign for an independent Basque state since the 1960s has been blamed for about 800 deaths.