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Gram-negative bacterial 3-hydroxy fatty acids (3-OH-FAs) have received recent attention for their potential as palaeoclimate proxies. A novel temperature proxy, the ratio of anteiso to normal C₁₃ 3-OH-FA (RAN₁₃), has been proposed for sea surface temperature (SST) reconstruction in the North Pacific Ocean. However, whether this newly proposed temperature proxy is applicable to marginal seas with significant terrigenous input or tropical oligotrophic seas requires further investigation. Here, we analyzed the composition and distribution of 3-OH-FAs and evaluated the possible impact of various environmental parameters (SST, water depth, dissolved oxygen, salinity and nutrient concentration) on their distribution in marine surface sediments from the Bohai Sea (BS) and the South China Sea (SCS). In the BS, the potential source proxy, fractional abundance of anteiso 3-OH-FAs (average 17%), indicates 3-OH-FA geochemical signature are not greatly overprinted by terrigenous inputs. The relative abundance of long-chain 3-OH-FAs (C₁₅-C₁₈) are higher in the SCS (average 41%) compared to those in other seas (average 33% for all marine samples). Massive inputs of terrigenous organic matter to the BS likely result in overestimation of SSTs based on the RAN₁₃ proxy, and limited abundance of anteiso and normal C₁₃ 3-OH-FAs in the oligotrophic SCS may increase the uncertainty of the RAN₁₃ estimated SSTs. More importantly, we find that most short-chain 3-OH-FAs are temperature dependent, especially the fractional abundance of i-C₁₂, a-C₁₃, i-C₁₄ and n-C₁₄ with a high determination coefficient (R² > 0.60). Based on these newly …