Waitea circinata Warcup & Talbot, which is related to the anamorphic form-genus Rhizoctonia D.C., is a world wide distributed soil-borne fungal pathogen. Several molecular based studies have been published based on rDNA-ITS sequences to determine the phylogenetic relations between and within the different Rhizoctonia groups. It is generally accepted that phylogenies depending on a single gene may be misleading. In this study, we phylogenetically analysed three varieties of Waitea circinata (var. circinata, var. zeae and var. oryzae) using the nucleotide sequences of two commonly used markers 18S rDNA and beta-tubulin for identification. Our phylogenetic analysis clearly supported the distinction of the three varieties. In W. circinata var. zeae, we determined a total of three lineages, two of which are distributed worldwide and one is unique for Americas. We observed both of the global lineages in Turkey and due to their dispersion, the invasion of these two lineages to Turkey probably occurred in different periods of times. Additionally, our results in this study once again suggested the Americas as the origin for W. circinata var. zeae.