Faunal succession is the fundamental assumption underlying the practice of biostratigraphy. Computational biostratigraphic techniques have been developed in recent times which systematize the original methods and are able to deal with the large volumes of data which are collected in the modern era and the expected increase of biostratigraphic contradictions. Despite the increase in sophistication, this paper will show that fossil time ordering cannot be uniquely determined from the fossil record—faunal succession remains a mere assumption, which may not be formally valid for fossils buried during the Genesis Flood. That fossil associations could reflect processes other than evolutionary developments over geological time is not considered. In this paper, I describe the computational algorithms necessary to test faunal succession from the observed ordering and associations in the fossil record. This also allows for direct comparison of models for generating order during the Flood without assuming faunal succession. I also offer a mathematical proof of the non-uniqueness of fossil seriations.