Lipid biomarkers of seep carbonates and sediments retrieved from the Dongsha area, Shenhu, Site F and Haima in the South China Sea (SCS) over the last two decades were studied. Biomarker inventories, microbial consortia, seepage dynamics, and biogeochemical processes of anaerobic oxidation of methane (AOM), aerobic oxidation of methane (AeOM), and oxidation of non-methane hydrocarbons, were reconstructed. Authigenic carbonates contained varying contents of 13C-depleted archaeal and bacterial biomarkers, reflecting their formation as a result of AOM under varying conditions. Except for the typical isoprenoids found in various cold seeps worldwide, 3,7,11,15-tetramethyl hexadecan-1,3-diol and two novel sn2-/sn3-O-hydroxyphytanyl glycerol monoethers with notable 13C-depletion were observed in authigenic carbonates obtained from Haima, which are most likely hydrolysis products of archaea-specific diethers. Furthermore, molecular fossils, compound-specific δ13C values, and mineralogies, were used to trace dominant microbial consortia, seepage activities, and environmental conditions in the cold seep ecosystems of the SCS. In this chapter, the archaeal and bacterial lipid biomarker geochemistry of methane seeps is systematically introduced. AOM, AeOM, oxidation of non-methane hydrocarbons, oil degradation, and the diagenetic fate of glycerol ethers, are further summarized.