Rice (Oryza sp.) agriculture sustains vast numbers of people and, despite great advancements made in recent years, questions about its origins and spread throughout Asia remain unanswered. This study uses sedimentary biomarker, stable carbon isotope and palynological analyses to investigate early rice agriculture in the Yangtze delta, a region where rice agriculture emerged at least 7000 years ago. Accelerator mass spectrometer (AMS) ¹⁴C dating reveals the age of sedimentary section to be between c. 6000 and 1800 cal. BP. Widespread clearing of forest vegetation c. 2400 cal. BP, is the earliest major human influence detected in the Qingpu record. Following this, rice agriculture probably dominated the Qingpu area. Evidence supporting rice agriculture after c. 2400 cal. BP is provided by increased Poaceae and Cereal-type taxa, which occur with high concentrations of plant wax n-alkanes with a dominant C₃ plant origin (C₂₇—C₃₁ with odd/even preference, δ ¹³C —29.8‰ to —36.3‰). Also, high concentrations of a C₂₀ highly branched isoprenoid (HBI) thought to be from epiphytic algae associated with rice agriculture occur after c. 2400 cal. BP. ¹³C-depleted diploptene (in high concentrations) and ¹³C-depleted C₃₁ 3b-methyl-hopanes of methanotrophic bacterial origin also occur after c. 2400 cal. BP. The strong methane cycle detected in the trench sediment may have provided an alternative CO₂ source for plants and algae associated with rice agriculture.