Cercospora Leaf Spot (CLS) of Swiss chard (Beta vulgaris L. var. cicla) remains an important foliar disease worldwide, yet the causative agent Cercospora beticola genetic variability remains incompletely understood in Botswana. To assess the diversity of C. beticola from diseased Swiss chard in southern Botswana, 78 isolates from two farms were analyzed. C. beticola was isolated from Swiss chard at very high frequencies from both Bokaa (91%) and Glen Valley (86%) farms. However, statistical analyses indicated that the isolation rate of the pathogen was not affected by the sampling location (p=0.01, p>0.01). Phylogenetic analyses revealed that the 18 sequenced C. beticola isolates clustered into four major classes, which could not be differentiated by the sampling location. Similarly, genetic analysis revealed high genetic diversity of C. beticola strains from the two farms, accounted for by within population diversity (greatest pairwise distance=0.004). The results presented herein underscore the importance of assessment of genetic diversity of pathogens which may be important in targeted control and management of plant diseases.

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