In-situ trace element analyses of fluorapatite, calcite, dolomite, olivine, and phlogopite have been undertaken on representative phoscorite and carbonatite rocks of the Palaeoproterozoic Phalaborwa Complex. Textural and compositional characterization reveals uniformity of fluorapatite and calcite among most of the intrusions, and seems to favor a common genetic origin for the phoscorite-carbonatite association. Representing major repositories for rare earth elements (REE), fluorapatite and calcite exhibit tightly correlated light REE (LREE) abundances, suggesting that partitioning of LREE into these rock forming minerals was principally controlled by simple igneous differentiation. However, light rare earth element distribution in apatite and calcite cannot be adequately explained by equilibrium and fractional crystallization and instead favors a complex crystallization history involving mixing of compositionally distinct magma batches, in agreement with previously reported mineral isotope variability that requires open-system behaviour.