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Investigating animal gut microbiomes can lead to a better understanding of their foraging preferences and their overall health. In this study, the fecal and cloacal microbiomes of 4 cold-stunned, frozen loggerhead Caretta caretta, 9 Kemp’s ridley Lepidochelys kempi , and 5 green sea turtles Chelonia mydas that stranded on beaches in Massachusetts, USA, were surveyed. Cloacal swabs and in situ fecal samples were collected from each turtle. From the extracted DNA, the hypervariable V1-V3 regions of the 16S rRNA gene were amplified with PCR, then sequenced using next generation Illumina MiSeq technology. Fecal and cloacal microbiomes were primarily composed of the phyla Proteobacteria , Bacteroidetes , and Firmicutes . Microbial communities varied significantly based on location of the gut sampled. Cloacal samples were largely dominated by Proteobacteria , while fecal samples appeared to have a greater distribution of taxa and higher alpha diversity. Green turtles had a higher abundance of Firmicutes and Bacteroidetes than Kemp’s ridley and loggerhead turtles, but a lower abundance of Proteobacteria . The information gained from this study contributes to knowledge of cold-stunned sea turtle gut microbiomes and may eventually be applied to rehabilitation efforts.