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Feral swine pose a substantial risk of disease transmission to livestock. Understanding the community of pathogens available for transmission by swine at both the local and regional scale is important for determining the risk feral swine pose to the cattle industry. We conducted a survey of blood and fecal microbes of 10 cattle from South Florida and 35 feral swine from 7 sites in the southeastern United States to address the following questions: 1) Which microbes do cattle and swine share? 2) What is the most frequent route of acquisition of shared microbes among cattle and swine? 3) Does proximity explain similarity in microbial community composition? We used a custom printed microarray spotted with 2 million sequences from >6000 microbes representing bacteria, viruses, protozoans and fungi. We detected 137 different microbial taxa in feral swine, 16 (12%) of which were shared with cattle. Two viruses shared among cattle and swine, herpesvirus, and T-cell lymphotropic virus, have strains that are pathogenic to cattle or swine. 56% of shared microbes were soil-associated bacteria; 38% were gut microbes, and the rest were bovine or porcine associated pathogens with a direct route of transmission associated with bodily fluids. None of the shared microbes in feral swine came from the same ranch as the cattle; however, among only feral swine, geographic distance explained microbial community similarity at the regional scale. Results suggest that the microarray approach is a fast and economical way to detect potential pathogens; however resolution to taxonomic level of strain or even species is lacking and requires further confirmation. Cattle and feral swine shared numerous soil and water-borne microbes in their feces illustrating the ease of pathogen acquisition from the environment.