The suspect, identified as Juad al-Buzruti, 23, was arrested in the town of Fuenlabrada, near the capital, the Interior Ministry said in a statement in Madrid on Monday.
"The detained man is believed to be a close collaborator" of the alleged cell linked to al-Qaida blamed for the 11 March 2004 attack, which killed 191 people and wounded 1900, the ministry said.
Al-Buzruti's arrest came just three days before Spain commemorated the first anniversary of the bombings and on the day an international conference on terrorism opened in Madrid.
Last November, in the first conviction in the bombings, a 16-year-old Spaniard was sentenced to six years in prison after pleading guilty to stealing and transporting dynamite used in the blasts.
Most of the 30 train bombing suspects under arrest or court supervision are North Africans described by High Court Judge Juan del Olmo as waging an Islamic holy war against the West.
In videotaped messages the bombers said they represented al-Qaida in Europe and said they were attacking Spain for sending troops to Iraq and Afghanistan.
Ten of the bombs went off at roughly the same time, three duds were destroyed by police and one - found 12 hours later in a police warehouse where it had been moved unintentionally - provided virtually all the breaks in the case, starting with the mobile phone used to trigger the detonator.