Glycerol dibiphytanyl glycerol tetraether lipids (GDGTs) have proven to be important biomarker lipids for specific archaeal lineages and their distribution is used as a paleotemperature proxy. In this study, we analyzed GDGTs in suspended particles in the water column of the Arabian Sea at different positions above, in and below the oxygen minimum zone (OMZ). GDGTs, both as intact polar lipid (IPL) and as core lipids, were detected throughout the water column but were most abundant at the upper part of the OMZ. Core lipid GDGTs, derived from non-living organic matter, were always much more abundant than GDGTs released by acid hydrolysis of an IPL fraction (IPL-derived GDGTs). Comparisons with 16S rRNA gene abundance showed that likely only 1-14% of total archaeal cells present were caught on the 0.7 lm filter used for lipid analysis. Despite this undersampling, the depth profiles of crenarchaeol core lipid with a phosphohexose or dihexose head group match previously reported profiles of (expressed) genes specific for ammonia-oxidizing Thaumarchaeota, such as 16S rDNA and amoA. In contrast, the crenarchaeol with a hexose head group as well as core lipid and IPL-derived crenarchaeol matched the genetic depth profiles much less, suggesting a contribution of GDGTs from non-living matter. TEX86 values of both core lipid and IPL-derived GDGTs increased from surface waters to the core of the OMZ, below which they decreased again, and did not correlate with in situ water temperature. In contrast, TEX86 values of IPL-derived GDGTs correlated well the relative amount of glycosidic GDGTs and were consistently higher than that those of CL GDGTs. This suggests that selective preservation of glycosidic GDGTs may mask TEX86 values of in situ produced GDGTs in deep marine waters.