The zooplankton fauna of freshwater systems of the Chihuahuan Desert was surveyed 2005–2008. Samples were obtained from habitats including natural lakes, ephemeral waters, springs, and reservoirs. Copepods were sorted and identified to species. Including previous surveys, a total of 38 species occur in the Chihuahuan Desert, the checklist includes 6 calanoids (1 Temoridae, 5 Diaptomidae), 24 cyclopoids (12 Eucyclopinae, 12 Cyclopinae), and 8 harpacticoids. These species were assigned to different biogeographic categories (i.e., cosmopolitan, Nearctic, Neotropical, potential endemics). Results indicated that the Chihuahuan Desert, a transitional biogeographic region in Mexico with both Nearctic and Neotropical influences, represents an interesting geographic and environmental realm characterized by a balanced mixture of elements from different origins and affinities. There is a relatively high proportion (23%) of species that probably are endemic.