Mitochondria are inherited through the maternal germline, and while paternal mitochondria elimination (PME) occurs following fertilization through autophagy, the mechanism(s) that assure paternal selectivity are not well understood. FUNDC1 (FUN14 domain containing1) is a mitochondrial outer-membrane protein that contributes to damaged mitochondria degradation following ischemia/reperfusion injury in mammalian cells. FNDC-1, the C. elegans ortholog of FUNDC1, is widely expressed in worm somatic tissues and mediates hypoxic mitophagy. Here, we report that FNDC-1 is not expressed in oocytes but strongly expressed in sperm, where it co-localizes with a mitochondria membrane marker. Loss of
fndc-1 retards the rate of both PME and paternal mitochondrial DNA degradation following fertilization. This effect is specific to the paternal germline, as maternal
fndc-1(lf) does not affect PME. In addition, the degradation of membranous organelles, a nematode-specific membrane compartment contributed by sperm that is also degraded through autophagy, is unaffected by
fndc-1(lf) in either maternal or paternal germlines, consistent with FNDC-1 being specific to paternal mitophagy and not general autophagy. Finally,
fndc-1(lf) does not impact the recruitment of LC3 homologs, LGG-1 and LGG-2, to mitochondria. Collectively, these findings represent the first report of a ubiquitin-independent mitophagy receptor playing a role in the selective elimination of paternal mitochondria.