Glycerol dialkyl glycerol tetraether (GDGT) compositions of suspended particulate matter in the water columns of two anoxic marine settings, the Black Sea and Cariaco Basin, were analyzed to better define the sources of GDGTs in marine environments. In deep anoxic waters the enhanced abundance of the conventional branched GDGT (B-GDGTs) and recently introduced overly- and sparsely-branched GDGTs (OB- and SB-GDGTs, respectively) indicated their in situ production by presently unidentified planktonic microorganisms favoring anoxic environment. The elevated concentrations of these branched GDGTs in anoxic waters were accompanied by an increase in their degree of methylation. Such a change in lipid composition may reflect either a microbial community shift or a physiological response of the source organism(s) to redox conditions, but nonetheless, confirms the in situ production of branched GDGTs in anoxic marine settings. In contrast to the B-GDGTs, which have originally been assumed to be of terrestrial origin, OB- and SB-GDGTs in marine sediments are more likely of anoxic marine origin. This notion is supported by a shelf-to-basin transect of surface sediments in the Black Sea, in which OB- and SB-GDGTs were restricted to distal sediments in the central anoxic basin. Even though the OB-, B- and SB-GDGTs are presumed to have related molecular structures, B-GDGTs were the only group that contained cyclopentane rings. The distribution of cycloalkylated vs. non-cycloalkylated B-GDGTs in the water columns of both the Black Sea and Cariaco Basin and surface sediments of the Black Sea suggests a primarily terrestrial origin for the cycloalkylated B-GDGTs but a mixed contribution from both terrestrial and marine sources for non-cycloalkylated B-GDGTs.