The chloroplast and mitochondrial genomes are essential for photosynthesis and respiration, respectively. RECA and RECG, which are plant-specific homologs of the bacterial homologous recombination repair proteins RecA and RecG, maintain organelle genome stability by suppressing aberrant recombination between short dispersed repeats (SDRs) in the moss Physcomitrella patens In this study, we analyzed the plant-specific factor RECX, a homolog of bacterial RecX that regulates RecA. RECX fused to GFP colocalized with mitochondrial RECA1 and chloroplast RECA2 on mitochondrial and chloroplast nucleoids, respectively. Knockout (KO) and overexpression (OEX) of RECX did not alter the P. patens morphological phenotype. Analysis of mitochondrial DNA, however, showed that products from recombination between SDRs increased significantly in RECX OEX mitochondria and modestly in RECX KO mitochondria. By contrast, analysis of chloroplast DNA revealed no substantial alteration in the number of products from recombination between SDRs in RECX KO and OEX chloroplasts. Yeast two-hybrid analysis revealed interactions between RECX and RECA1 and between RECX and RECA2. Expression profiles showed a positive correlation between RECX and factors maintaining the stability of both organelle genomes and RECA1 Collectively, these results suggest that RECX maintains mitochondrial genome stability, likely by modulating RECA1 activity, and that the compromised function of RECX induces mitochondrial genome instability.