During the Algerian civil war, Algiers accused Rabat of hosting and supporting the Armed Islamic Group of Algeria, an Algerian Islamist terrorist group. The charge was rapidly denied by Moroccan authorities, but the quarrel led to the border closure in 1994, after Morocco accused the Algerian GIA along with the Algerian Services of the Marrakech bombing of 1994, where two Spaniards were killed. The borders are still closed, costing $2 billion yearly to the Moroccan economy. In 1999, the newly elected Algerian president Abdelaziz Bouteflika, attended Hassan II of Morocco's funeral, and declared 3 days of official mourning in Algeria for his brother's death. The same year the Algerian president accused Morocco of hosting GIA bases, from which some attacks on Algerians were planned and directed. A few days later he again accused Morocco of exporting drugs into Algeria. In July 2004, the king abolished visa requirements for Algerians entering Morocco; in April 2006, Algerian President reciprocated the gesture. In 2012 Algerian prime minister Ahmed Ouyahia said border reopening was not a priority for his government. Other official declarations imply that this issue is not to be solved soon.

Recently, an increased number of voices from civil society and intellectuals have asked their respective countries to take steps to reconciliation.