Tadpole shrimp are known to be important animals in the ecology of ephemeral wetlands. In the northern Chihuahuan Desert of North America, the tadpole shrimp fauna is composed of possibly three species in the genus Triops, which have variously been referred to as species, subspecies, and intraspecific variation. Our results support the presence of three morphologically distinct forms, which will be referred to herein as T. newberryi, T. longicaudatus “short,” and T. longicaudatus “long.” We report analyses of Triops spp. sampled in summer 2008 from 14 natural playas and man-made flood retention ponds. Data were recorded on meristic counts and quantitative measurements of morphological features. We also sequenced portions of the mitochondrial COI and ND1 genes for 72 shrimp, including individuals from all three morphological forms and for multiple ponds for each form where possible. The three forms were morphologically distinct for multiple characters and molecular analyses showed large differences in DNA nucleotide sequence and the presence of multiple unique amino acid substitutions in each form. Finally, prior literature suggests the three forms exhibit different reproductive systems, with populations of T. longicaudatus “long” thought to be gonochoric (equal sex ratios and obligate outcrossing), T. longicaudatus “short” having only self-fertilizing hermaphrodites, and T. newberryi being androdioecious, having both self-fertilizing hermaphrodites and males. While these three forms may be sufficiently distinct in morphology, mitochondrial DNA, and reproductive life history to warrant elevation to species level, additional geographical sampling and an examination of the various type specimens are necessary for a formal taxonomic revision.