Amanita brunneipyramidalis, a new species of Amanita [subg. Amanitina] sect. Validae from India is described based on morphology together with molecular data. It is characterised by a clay-brown, sepia-brown to coffee coloured pileus covered with conspicuously concentrically arranged sub-conical to pyramidal warts, broadly ellipsoid to ellipsoid basidiospores 8.0-10.5 × 6.5-7.0 μm and occurrence in temperate mixed forest under Quercus semecarpifolia and Abies pindrow. Macro- and micro-morphological descriptions together with illustrations and phylogenetic analysis based on the nuclear ribosomal large subunit (nrLSU) is presented. Allied taxa have also been compared.