We used fishery-independent gillnet and longline surveys to document the elasmobranch and large teleost assemblages in the Florida Big Bend seagrass system and examine how ichthyofaunal assemblages were related to environmental factors across the region. A total of 159 paired gillnet sets were conducted in June through August from 2009 to 2012. The Big Bend, an expansive system nearly 300 km in length with seagrass from nearshore up to 20 km offshore, is inhabited by at least 13 species of elasmobranch and 56 species of larger teleost fishes during the summer. Five species dominate, including three species of sharks, two carcharhinids (Atlantic sharpnose sharks, Rhizoprionodon terraenovae Richardson, and blacktip sharks, Carcharhinus limbatus Mueller and Henle) and one sphyrnid (bonnethead sharks, Sphyrna tiburo Linnaeus), and two species of ariid catfishes (hardhead catfish, Ariopsis felis Linnaeus, and gafftopsail catfish, Bagre marinus Mitchill). We used a tiered community analysis approach which included hierarchical cluster analysis, indicator species analysis, and non-metric multidimensional scaling with environmental fitting using a Bray-Curtis dissimilarity matrix. Abiotic variables correlated with community structure included salinity, water clarity, and depth. Summer ichthyofaunal assemblages were spatially variable with a distinct southern zone where salinity and water clarity are consistently high relative to the rest of the system, and we hypothesize the observed patterns in community structure are related to a gradient of river influence in the Big Bend.