In this study we reconstruct sea surface temperatures (SSTs) using two lipid-based biomarker proxies (alkenone unsaturation index View the MathML sourceU37K′ and TEX86 index based on glycerol dibiphytanyl glycerol tetraethers) in 36 surface sediment samples from the Indonesian continental margin off west Sumatra and south of Java and the Lesser Sunda Islands. Comparison of measured temperatures (World Ocean Atlas 09) to reconstructed temperatures suggests that SST estimates based on View the MathML sourceU37K′ reflect the SE monsoon SST in the upwelling area south of Java and the Lesser Sunda Islands. Estimates based on TEX86 using the calibration for temperatures >20 °C (View the MathML sourceTEX86H) are up to 2 °C lower than View the MathML sourceU37K′-based SSTs. This offset is possibly related to either one or a combination of two factors: (i) the depth habitats of the source organisms and (ii) different seasonal production and/or seasonality of export associated with phytoplankton blooming triggered by primary productivity. In the non-upwelling area off west Sumatra, the alkenone-based SSTs are cooler than measured temperatures during the entire year, likely reflecting the limitations of the View the MathML sourceU37K′ proxy beyond 28 °C, while reconstructed temperatures based on View the MathML sourceTEX86H are consistent with mean annual SST.