Spanish officers with the help of French police seized Abdelmalek Tanem, 24, in the southern city of Almeria on Wednesday afternoon, the ministry said in a statement.
They said he was thought to have carried out "terrorist activities" in Syria with two jihadist factions: the Islamic State of Iraq and the Levant (ISIL), and the Al-Nusra Front.
He is suspected of serving as a "combatant" as well as a "facilitator" on the Syria-Turkey border helping other Europeans travel to join the group.
Spain has arrested hundreds of suspected Islamists in the decade since Al-Qaeda inspired bomb attacks killed 191 people on commuter trains in Madrid in March 2004.
Spanish security forces say they fear battle-hardened Islamist fighters may return from Syria under the influence of Al-Qaeda-inspired groups, presenting a threat of attacks in Spain.
Both Al-Nusra Front and ISIL were initially offshoots of the Al-Qaeda branch in Iraq before deteriorating ties between them in Syria erupted into violence.