Double-stranded breaks can be repaired by different mechanisms such as homologousrecombination (HR), classical nonhomologous end joining (C-NHEJ) and alternative endjoining (Alt-EJ). Polymerase Q (POLQ) has been proposed to be the main factor involved inAlt-EJ-mediated DNA repair. Here we describe the role of POLQ in DNA repair and gene targeting inPhyscomitrellapatens. The disruption of thePOLQgene does not influence the genetic stability ofP. patensnor its development. Thepolqmutant shows the same sensitivity as wild-type towards most of the genotoxicagents tested (ultraviolet (UV), methyl methanesulfonate (MMS) and cisplatin) with thenotable exception of bleomycin for which it shows less sensitivity than the wild-type. Further-more, we show that POLQ is involved in the repair of CRISPR-Cas9-induced double-strandedbreaks inP. patens. We also demonstrate that POLQ is a potential competitor and/or inhibitorof the HR repair pathway. This finding has a consequence in terms of genetic engineering, as in the absence of POLQthe frequency of gene targeting is significantly increased and the number of clean two-sidedHR-mediated insertions is enhanced. Therefore, the control of POLQ activity in plants couldbe a useful strategy to optimize the tools of genome engineering for plant breeding.