In this study we reconstruct sea surface temperatures (SSTs) using two lipid-based biomarker proxies (alkenone unsaturation index U37K' 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 U37K' 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 (TEX86H) are up to 2°C lower than U37K'-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 U37K' proxy beyond 28°C, while reconstructed temperatures based on TEX86H are consistent with mean annual SST. © 2014 Elsevier Ltd.