Abstract: A mega-pockmark, 1 500 m in diameter and 75 m in depth, is discovered on the east side of the Baiyun Sag, the South China Sea. Many irregular nodules are collected from the mega-pockmark and most of them characterized by fresh holes and seep passages. The mineral composition, microstructures, stable carbon and oxygen isotopes (δ¹³C and δ¹⁸O) of the five authigenic carbonates are used to trace the fluid source and their forming environment. Mineralogical study suggests that the five carbonates are all dominated by ferrous dolomite, followed by a detrital fraction, mainly composed of quartz and feldspar. The δ¹³C of the five carbonates falls in the range of -24.7‰~-10.9‰, indicating a primary source of 13C-depleted thermogenic methane. The δ¹⁸O of five carbonates varies between 5.6‰~6.9‰ V-PDB, indicating that the ¹⁸O-rich fluids are derived from the decomposition of gas hydrates and/or dehydration of clay minerals at depth. Gas hydrate may have existed in the sediment of the mega-pockmark. Ferrous dolomites in authigenic carbonates are formed in sediments and subsequently exposed to the seawater, indicating that the old methane seep was related to deep oil and gas seepage in the mega-pockmark. The live tubeworms and gas plumes in the pockmark suggest that methane seep is still active nowadays.