The genetic structure of Mycosphaerella musicola has never been investigated in Brazil to address epidemiologically related questions associated with yellow sigatoka. A total of 223 single‐conidium isolates from four regions (North, South, Zona da Mata and Triângulo Mineiro) of Minas Gerais State, Brazil, were used to assess the population genetic structure of M. musicola. Isolates were characterized regarding the frequency of the MAT1‐1‐1 or MAT1‐2‐1 idiomorphs and polymorphism at nine microsatellite loci. The mating‐type ratio in three of the four subpopulations was c. 1:1. A total of 87 alleles and 216 multilocus genotypes were identified. The overall population was in linkage equilibrium. Most (93.9%) genetic variation was detected within the subpopulations and there was weak differentiation between them. In total, eight genetic groups were detected and isolates of seven groups were present in all regions. The population of M. musicola in Minas Gerais seems to have high evolutionary potential: it is panmictic and both sexual reproduction and gene flow affect genetic variability. Strategies to avoid fungicide resistance should be enforced and breeding programmes need to consider quantitative resistance in the banana cultivars.
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