In a nearly 700-page document, investigative magistrate Baltasar Garzon issued international arrest orders for bin Laden and seven others suspected in the Sept. 11 hijackings.
Spain served "as a place or base for resting, preparation, indoctrinating, support and financing" of al Qaeda, Garzon said in the ruling.
The list of indicted suspects includes Tayssir Alouni, the Al-Jazeera journalist arrested Sept. 8 in Spain, and Imad Eddin Barakat Yarkas, who was accused of leading an al Qaeda cell in Spain and was arrested in Madrid in November 2001.
Six others believed to be in Spain also were indicted, but not all will be jailed, according to the order, which was obtained by The Associated Press. Garzon ratified jailing orders for 11 already in prison in Spain.
Garzon also accused the suspects of belonging to a terrorist group and other crimes, including weapons possession, tax fraud and forgery.
Other names on the indictment list include Ramzi Binalshibh, another core leader of the Hamburg cell that helped prepare the attacks. He was arrested in Pakistan in September 2002.
Along with Germany, Spain is known to have been an important staging ground for the Sept. 11 attacks. Accused ringleader and suicide pilot Mohamed Atta visited Spain in July 2001 and is believed to have held a key planning meeting with other participants in the northeastern Spanish region of Tarragona.
About 40 Islamic extremist suspects have been arrested in Spain since the attacks, although many were released for lack of evidence.
Garzon has been leading the investigation in Spain into alleged members of al Qaeda and other militant Islamic groups.
Garzon had Chilean dictator Augusto Pinochet arrested in London but failed in 1999 to take him to court. Britain ultimately freed the aging ex-despot on grounds he was unfit to stand trial.
Last month, he had requested that Buenos Aires extradite 40 men indicted in Spain for abuses during Argentina's "dirty war."
He also had focused on Spain's Basque separatist conflict, working to break up commando units of the armed group ETA.