Botrytis cinerea, the causal agent of grey mold, has high genetic diversity and a broad host range. In grape and Prunus spp., Botrytis causes a fruit rot, and fungicide spray are routinely used to prevent loss pre- and post harvest. Five hundred thirty-five isolates of B. cinerea collected from grape and Prunus spp. in 2012, 2016, and 2017 were genotyped using 18 microsatellite markers and the transposable elements (TE) Boty and Flipper. Only nine markers, were considered informative and retained for the final analyses. Four hundred ninety-eight of the isolates were tested for resistance to six or seven different fungicides, representing 5 classes. After clone correction, 323 multi-locus genotypes (MLG) groups were retained across the three years, and four genetic sub populations were detected. High levels of clonality were observed across the dataset. Significant pairwise differentiation was detected among years, locations, TE composition, and host. However, most of the differentiation observed was within a subpopulation, and not between subpopulations. No differentiation was detected among fungicide resistance isolates when compared against individual products. When resistance to different numbers of fungicides were compared regardless of the chemistry, significant little differentiation was detected among resistance to two fungicides and three or four fungicide chemistries.