This paper presents the first comprehensive morphological characterization and identification of the wheat populations collected on the Archipelago of Madeira and preserved at the ISOPlexis Germplasm Bank, the University of Madeira, Funchal. Fifty-two wheat populations representing Madeira's Triticum diversity and a wide range of ecological conditions were evaluated based on the biometrical and cytometrical traits. Forty-six traits related to plant morphology, cytological and grain characteristics were included in a multivariate analysis. Taxonomic identification of the collected materials revealed the presence of 3 species, 2 subspecies and 16 botanical varieties among the Madeiran wheat germplasm. The obtained results were confirmed by the multivariate analysis since all accessions were grouped in clusters corresponding also to different taxonomic levels. The detailed description of the Madeiran wheat landraces may contribute also to the protection of the existing Triticum diversity as well as support efforts of conservation of landraces, proper germplasm preservation and utilization.