Recent advances in molecular methods have revealed that the canine and feline gastrointestinal (GI) tracts harbor a highly complex microbial ecosystem, comprising several hundred different bacterial genera. We are just beginning to understand how these microbes interact with the host and thereby exhibit an influence that reaches beyond the GI tract. This paper reviews recent studies cataloguing the microbial phylo - types identified in the GI tracts of healthy dogs and cats and how this intestinal ecosystem is altered in gastrointestinal diseases.