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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 structural changes of the organic molecules themselves, as well as cross-linking between them (e.g., through reactive sulfur species). Both processes transform the original biomolecules into geomolecules. For the oxic environment, these intermolecular and intramolecular transformations also operate, but cross-linking may be less important since the labile, reactive component is rapidly removed. As such, one may expect a structurally better preservation of the more refractory initial biomolecules in the oxic environment. 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 Thalassiphora pelagica) for comparison. We assess the macromolecular structures of cysts from the Eocene ( ∼ 40 Ma) sulfidic 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 and show no signs of morphological modification, pyrolysis gas chromatography mass spectroscopy and micro Fourier transform infrared analyses show that their macromolecular characteristics are strongly different. Comparison with recent cysts shows that the cysts deposited in the sulfidic Rhine Graben show a strong additional contribution of long-chain aliphatic moieties and thus less diagenetic intermolecular cross-linking. The presence of organic sulfur identifies natural volcanization as one of the diagenetic processes. Furthermore, we observe a loss of bound oxygen and no trace of the original carbohydrate signature of the cyst wall biomacromolecule. The material deposited in the oxic sediments of the Kerguelen Plateau shows no traces of sulfurization. It shows a minor contribution of short carbon chains only and thus less diagenetic intermolecular crosslinking. Furthermore, a carbohydrate signature was still preserved evidencing a better molecular preservation of the initial biomacromolecule, supporting our initial hypothesis. This shows that excellent morphological preservation does not imply excellent chemical preservation. It also 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 and its isotopic signature. © 2020 Author(s).