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Macrophomina phaseolina infects a wide range of plant species. In the case of Phaseolus vulgaris (the common bean), the Fungus causes charcoal rot which can lead to severe losses especially under arid conditions. In order to combat the disease, it is necessary, to have information on the population structure of the pathogen in terms of pathogenesis on different species which may be grown simultaneously or successively a region. Previous reports have demonstrated the heterogeneity of the pathogen both in terms of morphological characteristics and molecular genotype; however no systematic attempt has been made to compare pathogenesis of different isolates in relation to genotype, species of origin or geographical location. With this aim 84 isolates of M. phaseolina from different plant species in different geographical regions of Mexico were analysed by inoculation on a set of P. vulgaris cultivars differing in reaction to the fungus and by determination of their amplified fragment length polymorphism (AFLP) genotype. Forty three distinct pathotypes were identified, only two of which were found in more than one species. All 84 isolates had distinct AFLP genotypes and cluster analysis showed a tendency of the isolates to form groups related to geographical origin or species of origin. (C) 2001 Academic Press.