This study was done to evaluate the microbial communities from the American alligator during feeding and fasting in wild and farm-raised individuals (2009-2011), to evaluate potential changes in communities. This study was conducted on the Rockefeller Wildlife Refuge, Grand Chenier, Louisiana. Samples were acquired from December 2009 through Spring 2011. Alligators undergo fasting from October to March, and samples were collected in the winter and spring from both farm-raised and wild salvaged individuals to assess the role of seasonality and rearing history on microbial community composition and structure. Samples were collected along the length of the gastrointestinal tract including the mouth, stomach, stomach contents, duodenum, ileum, colon, and feces to assess the lateral variation in microbes in physiologically distinct areas. Sampling included luminal contents as well as the underlying mucosa to fully evaluate host-associated microbes. The results are amplicon pyrosequencing libraries of single-direction reads generated using multiplexed, bar-coded primers targeting the Vi-V3 region of the bacterial 16S rRNA gene.