Authigenic carbon fluorapatite (CFA) is a crucial phosphorus sink in marine sediments and is the primary phosphorus-bearing mineral in submarine phosphorites. Understanding the genesis of CFA is of great scientific significance for understanding the changes in marine productivity, phosphorus cycling, and global climate and environmental effects throughout geological history. We overviewed the material sources, formation environment, and precipitation mechanisms of CFA in marine sediments. The enrichment of phosphorus in porewater involves the microbial decomposition of organic matter, the adsorption and release of phosphate by ferric oxyhydroxides, and the storage and utilization of polyphosphates by large sulfide bacteria. Fluctuations in redox conditions exert a significant influence on these processes. The formation of calcium phosphate (CaP) precursor phase is an important pathway for CFA precipitation. Moreover, the interface coupled dissolution and precipitation (ICDP) mechanism of CaP on calcium carbonate surfaces reveals the alteration genesis of CFA from a microscopic perspective. Based on these findings, future research directions for investigating the genesis of authigenic CFA in marine sediments are also proposed.