In this study, we analysed a collection of Waitea circinata comprising 20 isolates (17 var. zeae; one var. circinata and two var. oryzae) from different localities and hosts with macroscopic anastomosis tests, PCR-RFLP and phylogenetic analysis of the 18S-28S rDNA-ITS region. Macroscopic anastomosis was not useful for the identification of W. circinata isolates because all isolates, even those of the same variety, gave tuft reactions indicating unrelatedness. However, varieties of W. circinata showed unique RFLP patterns with HhaI, MseI and TaqI enzymes, suggesting that this molecular method may be suitable for quick identification. 18S-28S rDNA-ITS phylogeny revealed two main monophyletic groups within W. circinata var. zeae isolates. The first main monophyletic group appeared global as it contained isolates from Asia, the Americas and Europe, and the second main monophyletic group was only comprised of isolates from the Americas. Because the genetic diversity of W. circinata var. zeae isolates from the Americas was higher than that from other continents, it may have originated there and later it may have disseminated from Far East to Eastern Europe.