Wagnerite-Ma5bc polytype is found in a gneiss associated with cordierite-prismatine-bearing gneiss, northern Stornes Peninsula, Larsemann Hills, East Antarctica. Wagnerite coexists with apatite and both of them are present as rock-forming minerals. Ca depletion is not essential to the formation of wagnerite; sufficient Mg, P and F components, and a relatively low Ca/Mg ratio is critical,otherwise only apatite crystallizes. Strong anatexis of the quartzofeldspathic gneiss of the area results in differentiation and separate enrichment of leuco- and melanocratic components. P and F tend to accumulate in the mafic-rich melanocratic component, and when their abundance reaches certain concentration, wagnerite forms. It is perhaps the chemistry of the setting that controls the appearance of wagnerite,whereas the PT condition is responsible for the variety of wagnerite polytype. A disordered polytype crystallizes at relatively high temperature, then cools down slowly and transforms into one of the ordered polytypes, in this case, the Ma5bc polytype.