Allosaurus is one of the most famous theropod dinosaurs, but the validity and relationships between the different species have been confusing and often questioned. Portugal is relevant to the understanding of the genus in light of the discovery of A. europaeus ML415 from the Early Tithonian of Lourinhã and Allosaurus MNHNUL/AND.001 from Andrés. However, the exact classification and validity of these two specimens has always been controversial. The presence of Allosaurus in Portugal is strong evidence for a North America–Europe Late Jurassic dispersal, later supported by other taxa. A detailed cranial description and specimen-based phylogeny were performed and resolved many of the open questions: (1) The diversity of Allosaurus is limited to three named species: A. fragilis, A. europaeus, and A. jimmadseni. (2) Nine autapomorphies were found in A. europaeus, confirming the validity of the species. (3) Phylogenetic analyses place both Portuguese specimens in the genus Allosaurus, based on the following synapomorphies: jugal bone lateral view, relative heights of quadratojugal prongs, the dorsal prong is equal in height, the jugal bone in lateral view shows shallow accessory pneumatization of the antorbital fossa, the palatine pneumatic recess shape is small, and lacrimal horn morphology has a triangular horn. (4) The Andrés specimen is placed with the A. europaeus and they are considered here to be the same species, which is paleo-geographically and biochronologically congruent. (5) A. europaeus and A. jimmadseni are sister taxa and closer to each other than to A. fragilis. The genus is distributed in occurrences from the United States, Germany, and Portugal, and from the Late Kimmeridgian to the Late Tithonian, while the Cenomanian report from Japan is reidentified as Segnosaurus.