Abstract. Anoxic sediments as compared to oxic settings encompass a much higher proportion of relatively labile and thus more reactive organic matter, naturally giving rise to condensation reactions (such as vulcanisation) transforming the original biomolecules into geomolecules. For the oxic environment where the labile, reactive, component is rapidly removed, such transformation and condensation is much less likely so that one would expect a structurally much better preservation of the more refractory initial biomolecules. To test this hypothesis, initially identical biomolecules need to be compared between different preservational environments. Here, we use the species specific morphology of organic microfossils to assure a single initial biosynthetic product (the cysts of the fossil dinoflagellate species Thallasiphora pelagica) for comparison. We assess the macromolecular structures of cysts from the Eocene (~ 40 Ma) sulphidic Rhine Graben and the oxic Kerguelen Plateau and compare them with each other and the structures of recent cysts. While between the sites the T. pelagica cysts are morphologically identical, pyrolysis gas chromatography mass spectroscopy and micro Fourier transform infra red analyses show that their macromolecular characteristics are strongly different. The cysts deposited in the sulphidic Rhine Graben show a strong contribution of long-chain aliphatic moieties and organic sulphur, absent in the material deposited on the oxic Kerguelen Plateau. Comparison with recent cyst walls suggests a much better molecular preservation for the oxic depositional environment, confirming our initial hypothesis. This leads to the conclusion that the best preservation of molecular structure is not necessarily where most organic matter gets preserved, which, in turn, is important for understanding the nature and fate of sedimentary organic matter.