Staphylococcus aureus has been extensively studied, yet it remains unclear why certain individuals continually carry the bacteria while others do not. Livestock workers are known to be at an increased risk of S. aureus colonization, but have not been as studied as other high risk groups, including hospitalized patients, have been. Culture based studies have shown other bacteria may decrease the likelihood of S. aureus colonization. Here, we utilize 16s rRNA sequencing to better characterize the ecologic relationships between S. aureus and the other microbes in the nares and oropharynx in a population of livestock workers. A cross-sectional, epidemiological study was conducted enrolling 59 participants (26 of which had livestock contact) in Iowa. Participants were enrolled in one of four ways: from an existing prospective cohort study (n=38), from the Iowa Department of Natural Resources Animal Feeding Operations database (n=17), through Iowa county fairs (n=3), and through snowball sampling (n=1). We collected two sets of swabs from the nares and oropharynx of each participant. The first set of swabs was used to assess the microbiome via 16s rRNA sequencing and the second was used to culture S. aureus. We observed livestock workers to have greater diversity in their microbiomes compared to those with no livestock contact. In the nares, there were 26 operational taxonomic units found to be different between livestock workers and non-livestock workers with the greatest difference seen with Streptococcus and Proteobacteria. In the oropharynx, livestock workers with swine exposure were more likely to carry several pathogenic organisms. We also observed colonized livestock workers to be more likely to carry P. gingivalis which may act as a bridge allowing S. aureus to adhere to Streptococcus in the oral cavity. While we observed no significant differences when comparing colonized persons to non-colonized persons in either the nares or oropharynx, Corynebacterium was more abundant in the colonized persons. Colonized individuals also had greater diversity in their nasal microbiome compared to non-colonized individuals. However, when comparing persistently colonized persons to intermittently colonized persons, we found Corynebacterium argentorantense to be more abundant in the persistently colonized individuals. We hypothesized the genera present in the nares and oropharynx of S. aureus carriers would be different from that of non-carriers and there would be differences in the nasal and oropharyngeal microbiomes based on livestock contact and carrier state (persistent, intermittent, and non-carrier). While there were no significant differences between carriers and non-carriers, we were able to identify several operational taxonomic units that were different between livestock worker carrier and non-carriers as well as differences by carrier state. The results of this study are the first to characterize the livestock worker nasal and oropharyngeal microbiomes. Additionally, the results shed light onto several organisms that may be influential in S. aureus carriage. However, further studies are needed to better understand these relationships and determine causality.