TEX86 has been increasingly applied for sea surface temperature reconstruction. This proxy is derived from the relative distribution of glycerol dialkyl glycerol tetraethers (GDGTs). Recently, however, increasing evidence showed that TEX86 could be affected by multiple variables (e.g. seasonal or terrestrial input, methanotroph input). In this study, GDGTs and TEX86 were studied in water column and sediments of the Pearl River estuary and coastal South China Sea. The results exhibited 1) unusually low TEX86-derived temperatures in the transitional area, and 2) strong correlation between Ring Index (weighted average number of cyclopentane rings in GDGTs) and Marine Group II (MG II) Euryarchaeota. Lipid and molecular DNA both indicate that 1) archaeal community composition is the crucial factor to bias TEX86, and 2) MG II synthesize ringed GDGTs, which may alter TEX86 in the transitional area. Our study warns against using TEX86 for interpretation of the (coastal) sediment record.