Equine metabolic syndrome (EMS) is an ever-increasing problem in the equine industry, especially considering that it is a risk factor for the development of laminitis. Equine metabolic syndrome is similar to metabolic syndrome in humans, which has been associated with alterations in intestinal microbiota. However, no work to date has been published to characterize the fecal microbiota in the EMS horse to determine differences, if any, from the metabolically normal animal. Therefore, our objective was to characterize the fecal microbiota of horses with EMS compared with non-EMS controls. Ten horses were classified as having EMS, and 10 non-EMS controls were selected for this work. Equine metabolic syndrome was determined as: insulin resistance, general or regional adiposity, and a history of or predisposition to laminitis. Blood collection via jugular venipuncture was performed, along with an oral sugar challenge. Concurrent with blood collection, phenotypic measurements and fecal grab samples were taken. Fecal samples were used to extract DNA for next generation sequence-based analysis of the bacterial microbiota. Equine metabolic syndrome horses exhibited a decrease in fecal microbial diversity, and there were differences in overall community structure between EMS horses and controls. The operational taxonomic unit with the highest linear discriminant analysis effect size in association with EMS horses was a member of subdivision 5 of Verrucomicrobia incertae sedis (uncertain classification). Interestingly, the control group had an overrepresentation of genus Fibrobacter. These data demonstrate that EMS horses have differences in their fecal microbiota compared with controls.