Organic biomarkers were used to investigate the influence of seasonal changes in oxygenation and water chemistry on the distribution of archaea and bacteria in the water column and surface sediments of the continental shelf off central Chile (ca. 36°S), an area influenced by seasonal upwelling and the development of an oxygen minimum zone. We were interested in establishing if occurrence of archaea and bacteria responds to oxygenation and water chemistry for which we analyzed archaeal isoprenoid (i) and bacterial branched (br) glycerol dialkyl glycerol tetraethers (GDGTs). Our results combined with molecular data from a year round observational program at the same sampling site and depths indicatives the occurrence and dominance of the marine pelagic group Thaumarchaeota. Changes in the distribution of iGDGTs might be explained by (i) the presence of archaeal populations in sub-oxic waters, phylogenetically different from those in surface water, (ii) changes in the relative contribution of Euryarchaeota with depth, and (iii) a relationship between Thaumarchaeota and environmental factors other than temperature. Branched GDGTs were more abundant in the upper, oxic layer during the non-upwelling season, may be a result of higher river runoff, whereas their diversity was higher within sub-oxic waters. Our results indicate a vertical segregation of iGDGTs and brGDGTs, with predominance of archaeal biomarkers during the low productivity season.