Deserts are contradictions; while above ground terrestrial productivity is low, they support a remarkable degree of biodiversity and harbor large numbers of endemic terrestrial and freshwater taxa. Indeed the aquatic oases of the four North American deserts have been likened to a freshwater Galapagos for their potential biodiversity and ecological and evolutionary significance (Dinerstein et al., 2000). Unfortunately, little is known of the zooplankton communities of deserts. We surveyed >145 aquatic sites in the Chihuahuan Desert (both USA and Mexico) representing 13 broad categories of habitats, from small rock pools to large reservoirs. Our purposes included characterizing the rotifer community structure and identify phylogeographic patterns among selected taxa. Our survey yielded >250 species, which, according to Segers (2007), represents about 16% of known rotifer species. More information on this dataset can be found in the Freshwater Metadatabase - BFE_79 (http://www.freshwatermetadata.eu/metadb/bf_mdb_view.php?entryID=BFE_79).