Accurate species identification is a challenge in megadiverse regions, where morphology alone can lead to overestimation or underestimation of biodiversity. In this context, the incorporation of molecular approaches, such as DNA barcoding, has been useful in accurately estimating regional biodiversity, revealing cryptic diversity, and enabling identification by non-specialists. This study generated a molecular database of fishes for Parque Nacional dos Lençóis Maranhenses and adjacent areas, based on sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Haplotype analyses were conducted using Maximum likelihood (ML), and the delimitation of Operational Taxonomic Units (OTUs) combined the following methods: Kimura 2-parameter model (K2P), Assemble Species by Automatic Partitioning (ASAP) and Poisson Tree Processes (PTP) methods, using K2P ≥ 2