Sour rot is a disease complex produced by an interaction between grape berries and various species of yeast and acetic acid bacteria in the presence of Drosophila fruit flies. While yeast and bacteria are consistently found on healthy grape berries worldwide, we explored whether the composition of these epiphytic communities differed depending on the presence or absence of sour rot symptoms. Using high-throughput sequencing, we characterized the microbiome of sour rot-affected grapes from two geographical areas across two years. In 2015 and 2016, both healthy and sour rot-affected berries were collected from commercial and research vineyards in Geneva, NY and commercial vineyards in Tasmania, AUS. In this experiment, all associated organisms grouped together primarily by location, and not by presence/absence of symptoms or cultivar. The predominant difference between asymptomatic and symptomatic samples, regardless of location, was the abundance of Acetobacter species, which were significantly more plentiful in the symptomatic samples. Yeast genera such as Candida, Hanseniaspora, Pichia and Saccharomyces were abundant in both sets of samples, but varied by region. The consistent presence of yeast species and the increased abundance of acetic acid-generating bacteria is consistent with our understanding of their etiological role in sour rot development. In 2016, diseased grapes also were collected from vineyards in Fredonia, NY, and Modesto, CA. Consistent with our comparison study, all associated organisms again grouped together primarily by location. Yeast genera such as Candida, Hanseniaspora, Pichia and Saccharomyces were abundant in both sets of samples, but varied by region. The consistent presence of yeast species and the abundance of acetic acid-generating bacteria in both experiments is consistent with our understanding of their etiological role in sour rot development.