Some investigators suggest a similarity between the oral microbiota of dogs and humans. The in vivo assessment of ecologic relationships among bacterial species and between bacterial species and their habitat is difficult to carry out. Consequently, this aspect is often neglected in animal oral microbiological studies. This study aimed to examine the proportions of 40 bacterial species in samples from five intra-oral habitats in beagle dogs using checkerboard DNA-DNA hybridization. Microbial samples were taken from subgingival and supra-gingival plaque, the tongue, tonsils and cheek mucosa in seven beagle dogs. Samples were individually evaluated for their content of 40 bacterial species and the percentage of total DNA probe count was determined for each species, at each habitat. All tested species could be detected in all sampled habitats but each habitat had a distinct community structure. The microbiotas colonizing the hard surfaces in the oral cavity were quite different from the microbiotas colonizing the soft tissues. Bacterial species that are in humans considered to be periodontopathogens are present in high proportions. This study underlines the importance of the habitat and the host on the local microbial profile. (c) 2007 Elsevier B.V. All rights reserved.