Mesoscale eddies contribute to the distribution of resources for plankton to thrive but can also trap and isolate plankton communities resulting in rapidly vanishing resources. Nitrogen-fixing organisms, diazotrophs, provide a large amount of nitrogen for other organisms, particularly in large nutrient-depleted regions such as the subtropical gyres. However, how fine-scale structures with fast-changing environmental conditions, compared to large ocean regions, impact diazotrophs’ distribution remains largely unknown. Here, we investigated diazotroph diversity within the Gulf Stream and associated eddies, a region with intense eddy activity known for its significant role in nutrient transport into the North Atlantic Subtropical Gyre.