The Um Ghannam area lies within the core of Hafafit Complex, South Eastern Desert. This area is occupied mainly by granitic gneiss (orthogneiss). However, the granitic gneiss is extruded by swarm metarhyolite dykes and quartz veins. The studied metarhyolite dyke is classified into two distinctive zones. However, the intense degree of hydrothermal alteration can partition this dyke into weakly and extremely altered zones. According to the extraordinary diversity in color, this dyke is distinguished into gray to dark gray (weakly altered) and greenish (extremely altered) metarhyolite. Petrographical, mineralogical, and geochemical characteristics of the two distinctive zones are detected in a representative sample. Petrographically, the weakly altered zone is mainly represented by chloritization of primary biotite, garnet, and epidote, and argillitization of primary plagioclase. Although the extremely altered zone contains intensely altered remnants of the original rock, the extremely altered zone is distinguished by intense oxidation products (carbonate minerals and quartz, with significant amounts of secondary Cr-muscovite and hematite). The mineralogical studies are imposed on the millimeter and the micrometer scale in this important hydrogeothermal system. Except for Ca and Mg, most of the major elements are depleted at the extremely altered zone. However, the extremely altered zone is enriched in trace elements (Cr, Mn, Co, and Ni). The major elements of the extremely altered zone reflect the significant alterations (desilication, muscovitization, and carbonatization). These alteration processes have taken place in the hydrogeothermal system in the extremely altered zone. The geothermal fluid is responsible for these hydrothermal alterations. High fO2 and high temperature are characteristic features of this fluid. Then, the high-field-strength elements such as Zr, Ti, and P are depleted as a significant hydrothermal alteration. Also, nuclear elements with the anion of (CO3)2− can travel as molecular complexes (carbonates), as long as the chemical and structural conditions are suitable for the movement of these elements from the metarhyolite dyke to redeposit and accumulate in another geologic formation. The rare earth elements La and Ce, as well as Yb and Lu, are partially mobilized during intensity alterations. The rare earth elements (REEs) are depleted in abundance with enrichment of CO2 from the weakly altered zone to the extremely altered zone. The REE budget is decreased from the weakly altered zone to the extremely altered zone as 121.17 to (27.38 − 16.52), respectively. The significant depletion of ∑REEs is controlled by dissolution of monazite. Monazite breakdown and even apatite formation can be caused by alkaline fluid. This fluid is related to event and thermal stage. However, the negative anomaly of Eu can be noticed in all studied samples. Then, Eu anomaly may be formed from plagioclase fractionation. The weakly altered metarhyolite zone and orthogneiss have lower HREE/LREE (0.07–0.11), respectively, relative to the extremely altered metarhyolite zone (0.17 − 0.2). Even all studied samples at two significant zones are characterized by the enrichment of ∑LREEs relative to ∑HREEs.
