Distinguishing the sources of organic matters in marginal sea sediments is an important aspect of carbon cycle research. The authors report the contents of microbial biomarkers and the BIT index of 31 surface sediment samples from the western Yellow Sea near the old-Yellow River estuary. The results show higher BIT values (>0.15) for samples close to the old-Yellow River, and lower BIT values seaward. The contents of Branched GDGTs range between 5 and 94 ng/g, showing a similar spatial trend with the BIT index. Another biomarker ratio index of terrestrial organic matter, the ATB index (ratio of terrestrial odd-numbered n-alkanes to marine phytoplankton biomarkers), also reveals a similar spatial pattern with higher values near the old-Yellow River estuary and decreasing values seaward.