Aggression is a serious behavioral disorder in domestic dogs that endangers both dogs and humans. The underlying causes of canine aggression are poorly resolved and require illumination to ensure effective therapy. Recent research links the compositional diversity of the gut microbiome to behavioral and psychological regulation in other mammals, such as mice and humans. Given these observations, we hypothesized that the composition of the canine gut microbiome could associate with aggression. We analyzed fecal microbiome samples collected from a small population of pit bull type dogs seized from a dogfighting organization. This population included twenty-one dogs that displayed conspecific aggressive behaviors and ten that did not. Beta-diversity analyses support an association between gut microbiome structure and dog aggression. Additionally, we used a phylogenetic approach to resolve specific clades of gut bacteria that stratify aggressive and non-aggressive dogs, including clades within Lactobacillus, Dorea, Blautia, Turicibacter, and Bacteroides. Several of these taxa have been implicated in modulating mammalian behavior as well as gastrointestinal disease states. Although sample size limits this study, our findings indicate that gut microorganisms are linked to dog aggression and point to an aggression-associated physiological state that interacts with the gut microbiome. These results also indicate that the gut microbiome may be useful for diagnosing aggressive behaviors prior to their manifestation and potentially discerning cryptic etiologies of aggression.