The Yucatán Peninsula, Mexico is a carbonate platform well-known for extensive karst networks of densely stratified aquifer ecosystems. This aquifer supports diverse anchialine fauna, including species of the globally distributed atyid shrimp genus Typhlatya. Four species (T. campecheae, T. pearsei, T. dzilamensis and T. mitchelli) are endemic to the Peninsula, of which three are federally listed in Mexico. This first integrative evaluation [i.e., molecular (public and newly generated), morphological, broad geographic and type locality sampling, and environmental data] of Yucatán Typhlatya reveals considerable species identity conflict in prior phylogenetic assessments, broad species ranges and sympatry within cave systems, five genetic lineages (three known and two new to science) with the endangered T. campecheae herein classified as junior synonym of the vulnerable T. pearsei. Ancestral/divergence reconstructions support convergent evolution of a low-salinity/stenohaline ancestor of a post-Paleogene arc Yucatán+Cuba Typhlatya clade within a euryhaline/anchialine-adapted atyid clade, and secondary adaptation of the coastal-restricted euryhaline [2-37 psu] T. dzilamensis (unknown conservation status), of which the remaining four species lineages are low-salinity/stenohaline adapted found in both inland and coastal regions. This study demonstrates the need for integrative/interdisciplinary approaches when conducting biodiversity assessments in complex and poorly studied aquifers.