Abstract The lipid biomarkers of hopanoids in cold seep carbonates from the South China Sea continental slope were investigated by gas chromatography–mass spectrometer (GC–MS) and gas chromatography-isotope ratio-mass spectrometer (GC-ir-MS). The distribution of hopanes/hopenes shows a preference for the ‘biological’ 17β(H), 21β(H)-over the ‘geological’ 17α(H), 21β(H)-configuration. This interpretation is in agreement with the strong odd–even preference of long-chain n-alkanes in those samples, suggesting that the ββ hopanes may be the early diagenetic products of biohopanoids and the αβ, βα configurations of hopanes were mainly derived from allochthonous sources contributing to the organic matter of the carbonates. In terms of hopanoid acids, the C30 to C33 17β(H), 21β(H)-hopanoid acids were detected with C32 17β(H), 21β(H)-hopanoid acid being the most abundant. However, there is a significant difference in stable carbon isotopic compostions of the C32 17β(H), 21β(H)-hopanoic acid among samples (−30.7‰ to −69.8‰). The δ13C values match well with the carbon isotopic compositions of SRB-derived iso-/anteiso-C15:0 fatty acids in the samples, which strongly depend on the carbon utilization types by microbe. The most abundant compound of hopanols detected in the samples, C30-17β(H), 21β(H)-hopanol, may be a good indicator of diagenetic product of type I methanotrophs. The molecular and carbon isotopic compositions of hopanoids demonstrate clearly that there is a combination contribution of both SRB and type I or type X methanotrophs to the source organism in the seep carbonates from the South China Sea continental slope.