The　circadian　system,　which　has　a　period　of　about　24　h,　is　import　for　organismal　health　and　fitness.　The　molecular　circadian　clock　consists　of　feedback　loops　involving　both　transcription　and　translation,　and　proper　function　of　the　circadian　system　also　requires　communication　among　intracellular　organelles.　As　important　hubs　for　signaling　in　the　cell,　mitochondria　integrate　a　variety　of　signals.　Mitochondrial　dysfunction　and　disruption　of　circadian　rhythms　are　observed　in　neurodegenerative　diseases　and　during　aging.　However,　how　mitochondrial　dysfunction　influences　circadian　rhythm　is　largely　unknown.　Here,　we　report　that　Drosophila　prune　(pn),　which　localizes　to　the　mitochondrial　matrix,　most　likely　affects　the　function　of　certain　clock　neurons.　Deletion　of　pn　in　flies　caused　decreased　expression　of　mitochondrial　transcription　factor　TFAM　and　reductions　in　levels　of　mitochondrial　DNA,　which　resulted　in　mitochondrial　dysfunction.　Loss　of　pn　decreased　the　amplitude　of　circadian　rhythms.　In　addition,　we　showed　that　depletion　of　mtDNA　by　overexpression　of　a　mitochondrially　targeted　restriction　enzyme　mitoXhoI　also　decreased　the　robustness　of　circadian　rhythms.　Our　work　demonstrates　that　pn　is　important　for　mitochondrial　function　thus　involved　in　the　regulation　of　circadian　rhythms.