The southeast Missouri iron metallogenic province contains a remarkable wealth of historically important Fe, Cu, Au, and rare earth element (REE) deposits including the Pea Ridge iron oxide-apatite-rare earth element (IOA-REE) deposit and the Boss iron oxide-copper-gold (IOCG) deposit. These deposits are coeval with silicic and intermediate composition magmatism in the St. Francois Mountains terrane. Magmatism, iron-oxide (±Cu, Au, Co) and apatite formation, and REE mineralization overlapped in space and time, but the specific role of regional magmatism in the metallogenesis of these deposits remains unclear and basic petrogenetic models are still debated. We report results from high-spatial resolution textural and geochemical analyses of apatite from regional igneous and ore rocks to elucidate their petrogenetic histories and evaluate deposit models. Backscattered electron and spectral cathodoluminescence imaging of apatite reveal no primary igneous zoning, but show different domains with intricate rims and dissolution/reprecipitation textures, each with distinctive REE patterns in many samples. Apatite from all samples are nearly endmember fluorapatite containing up to ~1.3 wt% Cl and F/Cl ratios span nearly three orders of magnitude. Fresh igneous fluorapatite contain low Na2O (0.15 wt%) while most Pea Ridge ore samples contain higher Na2O (up to ~0.45 wt%), and concentrations of sulfur in fluorapatite of all types are generally moderate to low (0.3 wt% SO3). Significant amounts of Fe (60,000 ppm), Mg (30,000 ppm), Mn (7,000 ppm), and Sr (12,000 ppm) are contained in fluorapatite of all sample types, and they also have moderate amounts of As (4,000 ppm), Ba (2,000 ppm), Th (400 ppm), and U (80 ppm). Fluorapatite show an extraordinarily large range of REE (~0.1-2.0 wt%) and Y (~100-7000 ppm) concentrations. While fresh igneous fluorapatite share many geochemical features with metasomatized igneous fluorapatite and ore-stage fluorapatite from the Pea Ridge IOA and Boss IOCG ore zones, they also have distinct geochemical signatures that are indicative of unique trace element partitioning and substitution mechanisms. These distinguishing textural and geochemical signatures preclude ore-zone fluorapatite genesis directly from a magma (i.e., crystallization directly from a silicate melt) but are permissive of ore-zone fluorapatite formation by magmatic-hydrothermal fluids derived from the regional magmas. Basinal brines may play an important role in the formation of fluorapatite, especially from the Pea Ridge hematite and Boss magnetite-rich zones. Fluorapatite from different ore zones likely formed by crystallization during pulses of hydrothermal fluids with varying Cl-, Na-, and F-contents, which fundamentally controlled the carrying capacity and solubility of REE+Y and generated geochemically distinctive generations of fluorapatite. Exploration geologists using fluorapatite trace element geochemistry to identify IOA and IOCG deposits should proceed with caution, as more high-quality data from these deposits are needed to improve multivariate discrimination analysis. Fluorapatite from IOA/IOCG deposits can be reasonably discriminated from that of other mineral deposit types (e.g., porphyry/epithermal, skarn, orogenic), but no criteria successfully discriminate yet between IOA and IOCG deposits.