The objectives of this study were (a) to evaluate skin biopsies of udder sores and negative control cows for the presence of mange and nonbacterial pathogens via histopathology and (b) to identify and compare bacterial abundance in the lesions of cows with udder sores and from the skin of healthy controls from the same farms. Cows from 3 dairy farms with (n = 23) and without (n = 12) udder sore lesions were enrolled, and punch biopsies (23 lesions, 23 negative control samples of cows with lesions, and 12 control samples of cows without lesions) were collected. The biopsies were evaluated histopathologically, and their 16S metagenome was analyzed. No signs of mange or viral or fungal infections were detected histopathologically in any samples. The α diversity of microbial populations decreased in lesions, across all farms, and the abundance of spirochaetes did not notably change, compared with controls. However, compared with control samples, the microbial fractions of Fusobacterium, Helcococcus spp., Anaerococcus spp., Porphyromonas spp., Prevotella spp., and Trueperella spp. increased several-fold in lesions. In summary, our results suggest that spirochaetes, viruses, and mange are unlikely to cause udder sores. Instead, sores were associated with a marked increase in the abundance of Fusobacterium, Helcococcus, Anaerococcus, Porphyromonas, Prevotella, and Trueperella. Future studies are needed to determine which of these bacteria initiates this polymicrobial infection.