Flying fishes (family Exocoetidae) are important components of epipelagic ecosystems and are targeted by fishing fleets in the Caribbean Sea and elsewhere. However, owing to their anti-predator behavior and habitats, their ecology, abundance, and distributions are only partially known. From September 20 to October 6, 2011, we conducted a series of surveys over a large area (approximately 75,000 km2) of the northern Gulf of Mexico (87°W–90.5°W, 28°N–30°N). The surveys used an airborne lidar and vessel-based sampling, supported by near real time satellite observations of oceanic conditions. The aerial survey was conducted from a fixed wing aircraft that flew repeated surveys day and night, enabling data collection that was both broad-scale and synoptic. Vessel-based sampling included quantitative visual observations, trawl sampling, and qualitative dip-netting for species identifications. The combined surveys identified large aggregations of epipelagic organisms dominated by flying fishes. Large numbers of jellyfish (Aurelia sp.) and low numbers of numerous other species were also observed. The putative flying fish aggregations had an average length scale of 6.1 km and an average population estimated at 10,000 individuals. While always near the surface, flying fish aggregations were slightly deeper at night than during the day and found most often off the continental shelf in warm water with low chlorophyll concentrations. At least three species were present: Hirundichthys rondeletii (Valenciennes, 1847), Cheilopogon melanurus (Valenciennes, 1847), and Prognichthys occidentalis Parin, 1999. This combination of aerial and surface surveys afforded repeated synoptic, ground-truthed data collection over a large area and indicates that this method could be useful for surveying such mobile epipelagic fishes.