Primary almandine and spessartine-rich garnet and zinnwaldite phenocrysts occur along with feldspar (plagioclase and sanidine) phenocrysts, in the rhyolite of Profitis Ilias, which is located on the SE coast of the island of Chios, Greece. The distinctive mineralogical composition of this rhyolite is described. Although formed in the back-arc tectonic environment of the Aegean volcanic arc, the Profitis Ilias rhyolite shows significant trace element compositional differences when compared with typical arc or back-arc volcanic rocks of the area. It shows extreme depletion in Sr and Ba and enrichment in Nb and Mn, and has much more affinity with A-type granites and particularly Li-mica granites. Apparently, both zinnwaldite and spessartine-rich garnet can be generated as primary phases from a granite melt enriched in volatile constituents at low P-T. This granite melt could be the residual product of an unexposed, earlier formed, typical back-arc granite of the area, enriched in volatile constituents from a subcrustal source above the active mantle of the eastern Aegean area. The extensive and deep faulting in the broad eastern Aegean lithosphere section would have facilitated the rapid ascent of that volatile-enriched granite melt, the parent of the Profitis Ilias rhyolite.