ABSTRACT Morphological characters of species are essential for assessing the functional structure of a fish assemblage, since differences between them, for example in body shape, are related to many functional and ecological traits (e.g., swimming, search for food, striking and capturing prey, evading predators, spawning). Globally, tidal flats are relevant to fish assemblages by offering feeding, refuge, and reproduction grounds. To analyze the morphofunctional structure of the fish assemblage from a tidal flat on the Brazilian coast, we conducted standardized sampling using nine different fishing gears. The geometric morphometric method was applied to describe the fish shapes and verify the morphological structure of the assemblage. Here, we present the influence/susceptibility of each gear type on the morphological diversity of the fish assemblage. The results indicated that beach seine, otter trawl, marginal encircling gillnet, and fish traps, together, were the most effective gears to represent the maximum morphological variability of fish inhabiting that tidal flat. Moreover, the assemblage showed high morphological redundancy considered as a resistance of the ecosystem for avoiding functional diversity loss, emphasizing the importance of complementary gear use when determining fish assemblages in a conservation context.