Abstract
Throughout history, species within the genus Entamoeba have been described using criteria that were not always applied consistently, resulting in an often confusing and controversial taxonomy. Several factors contributed to this situation, including the limited number of morphological characters available for taxonomic studies, overlapping host ranges, mixed infections, and a cosmopolitan distribution associated with human and animal movements. The incorporation of genetic data as diagnostic and differential criteria during the second half of the twentieth century enabled the recognition of cryptic species and the proposal of new taxa; however, significant taxonomic issues remain unresolved. This review summarizes the historical development and major controversies in the taxonomy of Entamoeba, from its origins in the late nineteenth century, when morphology and host association were the available criteria, to the present day, in which molecular approaches provide a more realistic view of species diversity and interspecific relationships. Based on this analysis, general principles are proposed as a pragmatic synthesis to guide future taxonomic work on Entamoeba, emphasising lineage-based species delimitation, the central role of molecular evidence when diagnostic morphology is lacking, the contextual value of host data, and the need for nomenclatural decisions grounded in biological evidence and historical rigour.