Crane flies are the most diverse group within Diptera, but they are rarely studied in coastal ecosystems. Considering the scarcity of information on the biology and ecology of this group in the Neotropics, and the sparse literature available for taxonomic identification, we developed a descriptive checklist that incorporates morphology and DNA barcoding. We also created a generic identification key for crane flies of southern Brazilian salt marshes. We sampled crane flies continuously at three areas along the Patos Lagoon salt marshes over one year. A total of 14 genera/subgenera, 6 species, and 12 morphotypes belonging to Limoniidae and Tipulidae were identified. Distribution ranges of Symplecta cana (Walker, 1848) and two Ormosia Rondani, 1856 species were expanded. mtDNA COI sequences were compared to the BOLD and NCBI databases, but were matched only at the family level. Therefore, we provided sequences to both platforms, updated to the genus level. We found low (0.00-0.03) intraspecific and high (0.11-0.25) interspecific molecular differences indicating that the mtDNA COI region is adequate for distinguishing species within the Tipuloidea. The Dicranomyia Stephens, 1829 species complex showed low genetic difference, indicating that they could be one species with high morphological plasticity. This study will serve as a basis for future research on insects of Neotropical salt marshes.