Suspended particulate organic matter (POM) from the of the Anaximenes seamount (summit at 35º25.6N, 30º09.6E; ~680 m water depth), and a far away control site (Rhodes Basin; 35º55.0N, 28º48.0E; ~4430 m depth) was collected at three depths (50 m, 150 m and 15 m above bottom), during the Meteor 71/1 cruise (11-24 December 2006) in order to assess the effect of seamounts on POM concentrations, quality and transport to depth. Particulate Organic Carbon (POC) concentrations at 50 m were variable close to the seamount (14±7 μg L-1 n=5); the lowest value however was at the control site (5 μg L-1). POC values converged to similar values at every site below the euphotic layer (0.5 – 3 μg L-1). Lipid biomarker compositions backed up by multidimensional scale analysis of the 50 most abundant compounds showed significant differences between the surface and deeper waters. These were driven by the disappearance of polyunsaturated fatty acids (PUFAs) and the dominance of zooplankton-related biomarkers at depth indicating modification of fresh phytoplankton POM. The euphotic layer of the control site had similar lipid composition to the deeper waters in the vicinity of the seamount. The results tentatively suggest a ‘seamount effect’ on the composition and concentrations of suspended POM, however temporal variability cannot be ruled out.