It functioned as one of the most important military strongholds for the indigenous Polisario Front guerrilla after the retreat of Spain from what was then Spanish Sahara.

The Polisario argues that this is the Sahrawi Arab Democratic Republic, an exile government operative in Tindouf, which was declared in February the following year.

During the 1975-91 war between Polisario and Morocco, there were several battles over control of Guelta Zemmur, the heaviest taking place on March 24–27 and October 13, 1981.

Presently, the town is controlled by Morocco as part of what it claims as its Southern Provinces, but its final status is yet to be determined.

The town is the birthplace of Sahrawi human rights defender Mohammed Daddach, who is Morocco's longest serving political prisoner.