KLR‐1 scientific deep borehole, drilled in the 1993 Killari earthquake region of Maharashtra (India), penetrated 8 m thick infratrappean sediments below a 338 m‐thick column of Deccan volcanics that rested over Neoarchean amphibolite to granulite facies mid‐crustal basement. Detailed palynological studies revealed the presence of characteristic Gondwana palynomorphs in sedimentary succession that include Plicatipollenites indicus, P. trigonalis, Parasaccites korbaensis, P. diffusus, Microbaculispora indica, Cyclobaculisporites minimus, Cyclogranisporites barakarensis, C. gondwanensis, Jayantisporites pseudozonatus, Leiosphaeridia bokaroensis, Latosporites sp., Verrucosisporites sp., cf. V. ambiplicatus and Striatopodocarpites gondwanensis. Qualitative analyses of palynomorphs would suggest an Asselian age (298–295 Ma) for their formation and burial in dysoxic to anoxic conditions. Recorded palynological assemblages correlate well with continental Lower Gondwana (Early Permian) sediments of India, as well as other Gondwana continents, indicating a larger extent of Gondwana sedimentation than hitherto known today. Petrological studies indicate the presence of two types of carbonate units that overly the crystalline basement. A relatively coarse‐grained sparry carbonate rock immediately overlies the basement (Sample KIL‐7). The size of the carbonate crystals in the sparite vary from 100 to 500 μm. This unit is overlain by an extremely fine‐grained micrite resembling lime mud (Sample KIL‐6). Micrite is made of carbonate grains with an average size of 10 μm. X‐ray diffraction studies indicate that calcite is the dominant carbonate mineral, while dolomite and quartz occur in minor amounts. Geochemical analyses indicate that in these two samples of carbonate rock that overlie the basement, CaO (33.38 to 38.16 wt %) is higher than MgO (16.0–23.85 wt%). These infratrappeans sediments are also characterized by stable carbon (δ13C) and oxygen (δ18O) isotopic ratios ranging from −1.59 to −8.74‰ and −9.12 to −13.50‰ versus PDB, respectively, thereby conforming to non‐marine fresh water deposits. These findings provide first evidences of reactivation and rifting of Dharwar intracratonic regions during earliest Permian Gondwana Period, which led to severe lithospheric mantle destruction, and massive regional uplift and erosion of the granitic‐gneissic upper crust. Large scale inland‐rifting during the Gondwana sedimentation period was possibly a prelude to India‐Antarctic breakup during the early Cretaceous.