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Resulting data were subjected to quality control steps, and analyzed for bacterial community richness and diversity, within\u2010 and between\u2010group dissimilarity, and relative taxonomic composition.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>High\u2010quality reads (2.22 million bp) resulted in a mean of 159\u00a0068 sequences per sample. Bacterial community evenness and diversity was high when compared to other species, and did not significantly differ when samples were grouped by dogs or eyes. As expected, within\u2010dog samples were more similar than between\u2010dog samples. Taxonomic classification revealed that &gt;95% of the community consisted of Firmicutes (34.9\u00a0\u00b1\u00a08.8%), Actinobacteria (26.3\u00a0\u00b1\u00a07.1%), Proteobacteria (26.2\u00a0\u00b1\u00a06.6%), and Bacteroidetes (9.4\u00a0\u00b1\u00a02.4%). Key members of the dog ocular surface microbiome, found in all dogs and corresponding to &gt;25% of all identified<jats:styled-content style=\"fixed-case\">OTU<\/jats:styled-content>s (operational taxonomic units), were part of the<jats:italic>Bifidobacteriaceae, Lachnospiraceae, Moraxellaceae, Corynebacteriaceae<\/jats:italic>families. Genera previously thought to account for the majority of the core ocular surface microbiome in the dog (<jats:italic>Staphylococcus<\/jats:italic>sp.,<jats:italic>Streptococcus<\/jats:italic>sp., and<jats:italic>Bacillus<\/jats:italic>sp.) were associated with only 2.63% of overall reads.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>This study shows the feasibility of conjunctival swabs and high\u2010throughput sequencing to profile the bacterial community structure of the canine ocular surface. 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