Different areas of the body provide different habitats for microbes. The epidermal surface of stingrays consists of spare dermal denticles covered by a thick layer of mucus. Denticles and mucus protect rays from the environment but also provide a home to symbiotic microbes. Mucus is metabolically expensive for the host to produce, but it provides a nutrient rich environment for microbes. Gills are site for gas and waste excretion in fish. Gills, like mammalian respiratory organs, are a common site for pathogen invasion and thus the microbiome is of extreme importance. Gut microbial communities are commonly used to assess health but are extremely invasive to collect. Cloaca microbiomes are commonly used as an alternative to gut microbiome sampling where faecal or gut microbiome samples are unobtainable. We collected skin, gill and cloaca microbiome samples from nine southern eagle rays (Myliobatis tenuicaudatus). We will use shotgun metagenomics to identify microbial taxa and functions associated with the skin, gills, and cloaca. We expect that the microbial communities of each body site will be distinct. We also expect the functional genes present in the microbiomes from the different body sites will be different. Differences in the functional potential will reflect different niches occupied by microbes at different body sites.