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Seamount phosphates are increasingly regarded as potential resources for rare earth elements (REE) and plus yttrium (REY). Carbonate fluorapatite (CFA) formed within seamount ferromanganese (FeMn) crusts is the most common seamount phosphate mineral. However, reports on the mineralogy and geochemistry of CFA are few and thus its origin and acquisition of trace elements are not well understood. In this study, we analyzed the major and trace elements of CFA in FeMn crusts collected from Western and Central Pacific seamounts to investigate the genesis of trace elements in the CFA. This is the first study to use in situ analytical techniques such as electron microprobe analyzer (EPMA) and laser ablation-inductively coupled plasma mass spectrometry (LA-ICP-MS) to analyze seamount CFA. We found that the CFA hosts abundant minor and trace elements and propose that ionic substitutions are responsible for the high contents of SO3, SiO2, REY, Sr, Na, Fe, and Mn in the CFA veins found in the FeMn crusts, i.e., SiO32− and SO42− substitute for PO42−, while REE3+, Y3+, Na+, Fe2+, and Mn2+ substitute for Ca2+. REE3+ substitutions for Ca2+ in the CFA are charge-compensated by Na+ substitution for Ca2+. Fourier transform infrared spectroscopy (FTIR) analysis shows that CO32– mainly substitutes for PO42− in the CFA crystal structure, and there is a minor substitution of PO42− by CO3F3−. Ocean water is the major source of the P and REY, which when precipitated as seamount CFA is characterized by high ∑REE (345 to 6016 ppm) and heavy-REE (HREE) enrichments. Monazite grains dispersed in the seamount CFA contribute trace amount of REY. These results shed light on the composition and element mobility of seamount CFA with economic potential, which also provides valuable insights into global ocean chemical cycling (e.g. REE).