Efforts to determine causative agents in mammary inflammation in dairy cows are critical to animal welfare and economic viability. Two key questions to address are 1) what factors are important in maintaining a healthy milk microbiota and 2) what factors lead to the manifestation of bacterial infection or inflammation. Quarter milk samples from 103 mostly Holstein cows were obtained from 2 different dairies in Idaho. Characterization of the microbial community was performed by culture independent Illumina sequencing of amplicons from the V1-V3 hypervariable region of the 16S rRNA gene to determine relative abundance of bacteria present. Almost 45% of the reads were unclassified at the genus level, showing one of the limitations of this study. From the cows, 350 quarters had low somatic cell count (SCC) (<200,000 cells/mL), 26 had mid SCC (200,000–400,000 cells/mL), 3 quarters omitted due to missing SCC. Milk microbial communities were characterized with major membership by genera such as Staphylococcus (5–20%), Corynebacterium (5–10%), and Clostridium XI (5%). Higher SCC quarters tended to have elevated amounts of Staphylococcus and Streptococcus. Using the nonnegative matrix factorization (NMF) methodology, the community structure was best described by Caryophanon, Coxiella, Gemella, and Luteipulveratus, though the contribution differed greatly between quarters, SCC, and dairy. Overall, diversity (Shannon Diversity) was similar across quarters within an individual (16.22 – 17.68) whereas the diversity markedly decreased as SCC increased (18.04, 12.16, and 11.50 for low SCC, mid SCC, and high SCC, respectively). This pattern was also reflected by dairy. The dairy with a larger number of mid and high SCC quarters and had an overall lower average diversity (12.43) relative to the other dairy (21.87). In summary, quarters, though independent glands, appear to be biological replicates of the system under healthy conditionsC. More work is needed to determine the various aspects of microbial community structure that may confer health or disease states for mastitis in dairy cows. This work was supported by the Idaho State Board of Education.