The Khatyspyt Formation in Arctic Siberia is one of only two carbonate settings with Ediacara-type fossils. As a potential hydrocarbon source rock, it contains abundant molecular fossils that may help to expand our understanding of these ecosystems. Unfortunately, however, the molecular fossil record in geological materials is commonly biased by secondary processes such as thermal maturation, migration of bitumen compounds or surface contamination. In this study, we evaluate the preservation of molecular fossils in a sample from the Khatyspyt Formation and elucidate their paleobiological meaning. Our results reveal that the organic matter is remarkably immature (oil window maturity) and shows little effect of biodegradation. Petrographic observations, exterior/interior experiments, and the similarity between free bitumen, mineral-occluded bitumen, and kerogen pyrolysate point to the syngeneity of the molecular fossils. Abundant hopanes, cyclohexylalkanes, and methyl-branched alkanes indicate a bacterial source of the organic matter, likely including cyanobacteria and anaerobic bacteria. At the same time, a carbonaceous compression fossil on top of the sample and abundant steranes indicate the presence of eukaryotes. The steranes show typical distributions for the Ediacaran (i.e., dominance of stigmastane). Given the exceptional preservation of the body fossils, trace fossils, and molecular fossils, the Khatyspyt Formation can be considered a fossil lagerstätte sensu Seilacher (1970: Begriff und Bedeutung der Fossil-Lagerstätten. Neues Jahrbuch für Geologie und Paläontologie, Monatshefte: 34–39). The combined analysis of sedimentary facies, paleontology (body, trace, and molecular fossils), and biogeochemistry will provide a more complete understanding of ecosystems with Ediacara-type fossils.