Cytoplasmic male sterility (CMS), which causes dysfunctions in pollen and anther development, is an agronomically important trait used for F1 hybrid breeding. CMS plants are often obtained by successive backcrossing between distantly related species, which triggers imbalanced interaction between mitochondrial and nuclear genomes. A mitochondrial gene, orf288, in a standard japonica rice ‘Nipponbare’ has a sequence similarity to WA352, a CMS-causing gene in WA-type CMS. Although it is not expressed in anthers of ‘Nipponbare’, ORF288 protein expressed in yeast has been reported to bind to COX11, a subunit of the cytochrome c oxidase complex, in the same manner as WA352 protein. Here we found that orf288 gene was highly expressed in the anthers of an African rice (O. glaberrima) CMS line with the cytoplasm of a japonica rice (O. sativa) ‘Taichung 65’, while orf288 RNA was not detected in the fertility restored line. To prove that orf288 is a CMS-causative gene, we produced the orf288-depleted ‘Taichung 65’ plants using mitoTALEN, and investigated whether the orf288-depleted cytoplasm conferred male sterility or not to O. glaberrima, because transformation of O. glaberrima was recalcitrant. The null segregants of the orf288-depleted ‘Taichung 65’ plants set seeds normally. They were backcrossed with O. glaberrima. The resulting BC4F1 plants lacking the ‘Taichung 65’-derived chromosomal segments were fertile. These results demonstrated that the orf288-depleted ‘Taichung 65’cytoplasm did not cause male sterility when backcrossed with O. glaberrima. We concluded that orf288 is a cryptic CMS-causing gene in japonica rice mitochondrial genomes. [Acknowledgements, JSPS KAKENHI JP20K21300, 21H02161 and 23K18016]