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Biodiversity conservation and the identification of conservation units among invertebrates are complicated by low levels of morphological difference, particularly among aquatic taxa. Accordingly, biodiversity is often underestimated in communities of aquatic invertebrates, as revealed by high genetic divergence between cryptic species. We analyzed PCR-amplified portions of the mitochondrial cytochrome c oxidase I (COI) gene and 165 rRNA gene for amphipods in the Gammarus pecos species complex endemic to springs in the Chihuahuan Desert of southeast New Mexico and west Texas. Our analyses uncover the presence of seven separate species in this complex, of which only three nominal taxa are formally described. The distribution of these species is highly correlated with geography, with many present only in one spring or one spatially-restricted cluster of springs, indicating that each species likely merits protection under the US Endangered Species Act. We present evidence suggesting that habitat fragmentation, long-distance colonization, and isolation-by-distance have occurred at different temporal and spatial scales within this system to produce the lineages that we report. We show that patterns detected in the G. pecos species complex also correlate with endemic fishes (Gambusia spp., pupfish) and hydrobiid snails. Our results provide clues important for future biodiversity investigations in geographically isolated aquatic habitats, and shed light on the understudied and underestimated levels of biodiversity present in desert spring systems. (C) 2009 Elsevier Ltd. All rights reserved.