Despite the broadly held view that mangrove forests provide crucial habitat to many species, including juvenile fishes, the lack of efficient methods for sampling within the complex structure of mangrove prop roots and pneumatophores has hampered our ability to study mangrove fishes, especially in turbid areas where visual sampling is not an option. Many studies of mangrove fish communities rely on the assumption that species captured in adjacent mudflats and open channels are also present within vegetated microhabitats. I conducted a multi-season study at six mangrove sites in the Gulf of Nicoya, Costa Rica to compare the performance of traditional fishing gears used in mangroves (cast nets and seines) with that of the centipede net—a commercial fishing technique used in mangrove areas in the South China Sea. Centipede nets captured more species and more unique species, and they had greater sample coverage than traditional gears. Sampling with centipede nets in combination with either cast nets or seines captured more species in fewer site visits than a conventional sampling regime using cast nets and seines. Sampling with all three gears yielded the highest estimates of true species richness, Shannon diversity, and Simpson diversity. Centipede nets performed well across a range of environmental conditions, but catch rates were negatively related to bank steepness, so samples may not be comparable across sites with extremely different steepness. The proportion of species caught exclusively in centipede nets was lower in the Gulf of Nicoya (22%) than in Dongzhai Harbor, China (32%), but this difference was likely driven by differences in study design. I recommend the use of centipede nets, whether in isolation or in combination with traditional techniques, to researchers seeking a comprehensive understanding of fish communities utilizing flooded mangrove habitats to guide effective conservation and management strategies.