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Cryptic structure of species complexes confounds an accurate accounting of biological diversity in natural systems. Also, cryptic sibling species often become specialized to different ecological conditions, for instance, with host specialization by cryptic parasite species. The fungus Microbotryum violaceum causes anther smut disease in plants of Caryophyllaceae, and the degree of specialization and gene flow between strains on different hosts have been controversial in the literature. We conducted molecular phylogenetic analyses on M. violaceum from 23 host species and different geographic origins using three single-copy nuclear genes (β-tub, γ-tub, and Ef1α). Congruence between the phylogenies identified several lineages that evolved independently for a long time. The lineages had overlapping geographic ranges but were highly specialized on different hosts. These results thus suggest that M …