Zooarchaeology is a field heavily integrated with many other disciplines, including zoology, biology, ecology, geology, history, and anthropology. The basis of the discipline lies in the zooarchaeologist’s ability to identify faunal remains based on analogy with known specimens, either from a comparative faunal collection or from experience. Yet, today many zooarchaeologists work in regions of the world without adequate comparative materials or in diverse settings with different research demands, such as contract archaeology or forensic laboratories. At the same time, advances in genetic research are restructuring the phylogenetic classification schemes of many taxa, calling into question the foundation of zooarchaeological analogy. In this chapter we argue that zooarchaeologists, who have never had specific disciplinary-wide “research standards”, should seek epistemological flexibility regarding specimen identification, evaluation, and correction to continue the scientific advancement of the discipline. We review past zooarchaeologists’ concerns regarding the nature of specimen identification and data sharing, discuss the dynamic nature of species reclassification in phylogenetics and its effect on zooarchaeology, and provide case studies of challenges zooarchaeologists face while trying to make identifications in diverse settings and with less-than-adequate resources. Finally, we discuss the importance of maintaining epistemological flexibility in the age of “big data”, where shared datasets of identifications cannot and should not be seen as immutable entities, but rather observations that are subject to reanalysis, change, and improvement as zooarchaeologists keep abreast of ongoing discoveries in their own field as well as those of related disciplines.