Polyunsaturated fatty acids (PUFAs) play numerous roles in living organisms but are also prone to rapid aerobic oxidation, resulting in the production of a wide range of isomeric metabolites called oxylipins. Among these, isoprostanes, discovered in the 1990s, are formed non-enzymatically from ω-3 and ω-6 PUFAs with 16 to 22 carbon atoms. Over nearly 35 years of research, two nomenclature systems for isoprostanes have been proposed and have evolved. However, as research progresses, certain aspects of the current nomenclature remain unclear and require further clarification to ensure precise identification of each metabolite and its corresponding parent PUFA. Therefore, we propose an update to the current nomenclature system, along with practical guidelines for assessing isoprostanoid diversity and identifying their PUFA origins.