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Olive scab caused by Venturia oleagineais one of the most important diseases of olive worldwide. The fungus infects young leaves and fruits by asexually produced conidia. The sexual stage and its importance in the epidemiology and genetics of the pathogen population is unknown. A collection of 52 fungal isolates was obtained from scabbed leaves collected in 16 orchards from three major regions in Uruguay. All isolates were identified as V. oleagineaby PCR with specific primers and sequence analysis of the TEF-1α gene region. Five colony morphotypes and different growing rates were observed on potato dextrose agar (PDA) medium. Universally primed polymerase chain reaction (UP-PCR) was successfully used for assessing the genetic diversity and population structure of the V. oleagineaisolates, whereas ISSR was unable to generate reproducible and polymorphic bands. Two populations genetically different were identified: [1] composed by 21 isolates mainly from Southern and South-Western regions; [2] composed by 31 isolates mainly from South-Eastern and Southern regions. Both populations showed a moderate gene diversity expressed as hNei= 0.163 and 0.212 for population [1] and [2], respectively. There was evidence of linkage disequilibrium in both populations, rejecting the null hypothesis of random mating as the predominant reproduction mode, a typical result of clonal populations. However, all isolates were genotypically different, an indirect evidence of recombination. We conclude that V. oleagineapopulations in Uruguay present a mixed mode of reproduction, a characteristic of many pathogens that are difficult to control.