Climate conditions in the westernmost Mediterranean (Alboran Sea basin) over the last two millennia have been reconstructed through integration of molecular proxies applied for the first time in this region at such high resolution. Two temperature proxies, one based on isoprenoid membrane lipids of marine Thaumarchaeota (TEX86H-tetraether index of compounds consisting of 86 carbons) and the other on alkenones produced by haptophytes (U-37(K') ratio) were applied to reconstruct sea surface temperature (SST). Both records reveal a progressive long term decline in SST over the last two millennia and an increased rate of warming during the second half of the 20th century. This is in accord with previous temperature reconstructions for the Northern Hemisphere. TEX86H temperature values are higher than those inferred from U-37(K'), probably due to differences in the bloom season of haptophytes and Thaumarchaeota, and reflect summer SST. The branched vs. isoprenoid tetraether index (BIT index) suggests a low contribution of soil organic matter (OM) to the sedimentary OM. The stable carbon isotopic composition of long chain n-alkanes indicates a predominant C-3 plant contribution, with no major change in vegetation over the last 2000 yr. The distribution of long chain 1,14-diols (most likely sourced by Proboscia spp. in this setting) provides insight into variation in upwelling conditions during the last 2000 yr and depicts a correlation with the North Atlantic Oscillation (NAO) index, providing evidence of enhanced wind induced upwelling during periods of a persistent positive mode of the NAO.