Abstract Archaea, often thriving in extreme habitats, are believed to have evolved efficient DNA repair pathways to cope with constant insults to their genomes. However, how these organisms repair DNA double-strand breaks (DSBs), the most lethal DNA lesions, remains unclear. Here, we show that replicative primase consisting of the catalytic subunit PriS and the noncatalytic subunits PriL and PriX from the hyperthermophilic archaeon Saccharolobus islandicus is involved in DSB repair. We show that the overproduction or knockdown of PriL increases or decreases, respectively, the rate of survival and mutation frequency of S. islandicus cells following treatment with a DNA damaging agent. The increase in mutation is attributed primarily to an increase in small insertions or deletions. Further, overproduction of PriL enhances the repair of CRISPR-generated DSBs in vivo. These results are consistent with the extraordinary ability of PriSL to promote annealing between DNA strands sharing microhomology in addition to the activity of the heterodimer in terminal transfer and primer extension. The primase-mediated DSB repair is cell-cycle dependent since PriL is barely detectable during the S/G2 transition. Our data demonstrate that replicative primase is involved in DSB repair through microhomology-mediated end joining in Archaea.