New O and Fe stable isotope ratios are reported for magnetite samples from high-grade massive magnetite of the Mesoproterozoic Pea Ridge and Pilot Knob magnetite-apatite ore deposits and these results are compared with data for other iron oxide-apatite deposits to shed light on the origin of the southeast Missouri deposits. The δ18O values of magnetite from Pea Ridge (n = 12) and Pilot Knob (n = 3) range from 1.0 to 7.0 and 3.3 to 6.7‰, respectively. The δ56Fe values of magnetite from Pea Ridge (n = 10) and Pilot Knob (n = 6) are 0.03 to 0.35 and 0.06 to 0.27‰, respectively. These δ18O and the δ56Fe values suggest that magnetite crystallized from a silicate melt (typical igneous δ56Fe ranges 0.06–0.49‰) and grew in equilibrium with a magmatic-hydrothermal aqueous fluid. We propose that the δ18O and δ56Fe data for the Pea Ridge and Pilot Knob magnetite-apatite deposits are consistent with the flotation model recently proposed by Knipping et al. (2015a), which invokes flotation of a magmatic magnetite-fluid suspension and offers a plausible explanation for the igneous (i.e., up to ~15.9 wt % TiO2 in magnetite) and hydrothermal features of the deposits.