Previous studies have indicated that the Yellow Sea underwent significant environmental changes during the Holocene, but many questions remain concerning the timing of the establishment of the modern circulation system, which would have major implications for the Yellow Sea ecosystem and carbon cycle. In this study, marine and terrestrial biomarkers were analyzed in Core YE-2 from a muddy area in the southern Yellow Sea to reconstruct Holocene environmental and phytoplankton community change. The content of three individual marine phytoplankton biomarkers (alkenones, brassicasterol and dinosterol) all display a similar trend, and their total contents during the early Holocene (362 ng/g) were lower than those during the mid-late Holocene (991 ng/g). On the other hand, the contents of terrestrial biomarkers (C27+C29+C31n-alkanes) during the early Holocene (1 661 ng/g) were about three times higher than those during the mid-late Holocene (499 ng/g). Our biomarker results suggest that the modern circulation system of the Yellow Sea was established by 5-6 ka, and resulted in higher marine productivity and lower terrestrial organic matter inputs. Biomarker ratios were used to estimate shifts in phytoplankton community structure in response to mid-Holocene (5-6 ka) environmental changes in the Yellow Sea, revealing a transition from a dinoflagellate-diatom dominant community structure during the early Holocene to a coccolithophore-dominant community structure during the mid-late Holocene. Previous studies have indicated that the Yellow Sea underwent significant environmental changes during the Holocene, but many questions remained concerned the timing of the establishment of the modern circulation system, which would have major implications for the Yellow Sea ecosystem and carbon cycle. In this study, marine and terrestrial biomarkers were analyzed in Core YE-2 from a muddy area in the southern Yellow Sea to reconstruct Holocene environmental and phytoplankton community change. The content of three individual marine phytoplankton biomarkers (alkenones, brassicasterol and dinosterol) all display a similar trend, and their total contents during the early Holocene (362 ng / g) were lower than those during the mid-late Holocene (991 ng / g). On the other hand, the contents of terrestrial biomarkers (C27 + C29 + C31n-alkanes) during the early Holocene (1 661 ng / g) were about three times higher than those during the mid-late Holocene (499 ng / g). Our biomarker results suggest that the modern circulation of the Yellow Sea was established by 5-6 ka, and resulted in higher marine productivity and lower terrestrial organic matter inputs. Biomarker ratios were used to estimate shifts in phytoplankton community structure in response to mid-Holocene (5-6 ka ) environmental changes in the Yellow Sea, revealing a transition from a dinoflagellate-diatom dominant community structure during the early Holocene to a coccolithophore-dominant community structure during the mid-late Holocene.