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Seiridium cardinale is regarded as the most important agent responsible for the disease of cupressaceous hosts referred to as Cypress canker. The fungus was first described in California and is currently reported in all continents. A recent study based on seven SSR loci has suggested that California populations may represent the source of the epidemic in the Mediterranean. In this study, 185 AFLP markers were used on an expanded sample size of 125 isolates to determine whether the Mediterranean population may indeed be derived from the California one and to compare the reproductive modes of populations in the two regions of the world. Additionally, amova, NJ, STRUCTURE, principal component analysis and β-tubulin sequence analyses were employed to infer the presence of genetic structure within and between populations. The distribution of pairwise AFLP similarity coefficients suggests Mediterranean populations are reproducing only clonally, while California populations are reproducing both clonally and sexually. amova indicates Mediterranean and California populations are currently genetically isolated, but NJ and STRUCTURE analyses both suggest ancestral Mediterranean genotypes belong to the California population. No alleles were private to either population, and the presence of identical or quasi-identical genotypes at large distances supports the notion that movement of infected cypress plants is responsible for the global spread of the disease. Surprisingly, STRUCTURE identified a second cluster of Mediterranean genotypes distinct from the basal mixed California- Mediterranean cluster. This second cluster either may have originated from the first one under the selection pressure imposed on the pathogen in the new Mediterranean environments or may be the result of a further introduction from California or elsewhere. Cumulatively, the evidence presented here suggests that S. cardinale may be native or long naturalized in California and that two genetically distinct groups are present in the Mediterranean, with obvious implications for further studies on this disease. [ABSTRACT FROM AUTHOR]