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Migratory birds travel long distances and use diverse habitats, potentially exposing them to a broad range of microbes that could negatively affect their health and survival. Gut microbiota composition may be related to organismal health especially during periods of impaired immunity due to stress, by functioning as a reservoir for potential pathogens. We provide an insight into the composition of the gastrointestinal microbiota in migratory Red Knot (Calidris canutus) and Ruddy Turnstone (Arenaria interpres) staging in Delaware Bay, USA, by analyzing fecal bacterial communities of three individuals per species with 16S rRNA clone libraries. In the 313 bacterial sequences we analysed from Red Knots, we identified 19 bacterial classes across 29 genera, and from the 218 Ruddy Turnstone sequences, we identified 11 bacterial classes across 17 genera. In Red Knots and Ruddy Turnstones, 27 and 41 % of all sequences were closely related to Campylobacter spp., which include several human pathogens. Only 5 of the 46 genera, and 8 out of 124 operational taxonomic units were shared between species, suggesting that gut microbial community structure can be species-specific under environmentally similar conditions. Our study provides baseline information that can be used in future studies to better understand diversity and function of gut microbes, and can be expanded to investigate how gut microbiota of migratory birds affects their body condition, immune function, and demographic performance.