There are three recognized species of Siphateles from the Great Basin; S. alvordensis, S. boraxobius and the tui chub, S. bicolor. One species, S. boraxobius, is endangered and one population of tui chub at Hutton Spring is threatened. Despite several morphological and molecular studies, the taxonomy and relationships of tui chubs are unclear. A recurrent theme in prior studies has been the possibility of translocation of tui chubs, especially into Summer Lake Basin, and probably by bait bucket introductions. I approached this problem by using cytochrome b (cyt b) sequences to define clades and constructed a neighbor-joining tree to examine relationships. Developmental ontogeny and adult meristic characters were used to corroborate clades, and microsatellites (nDNA) used to explore the possibility of hybridization among Summer Lake Basin fish and those from surrounding basins. The cyt b tree recovered a basal polytomy containing a western clade from Sycan Marsh, an eastern clade from the Alvord Basin, and S. bicolor. The Sycan Marsh clade was represented by two fish and requires additional research. Within the Alvord Basin, S. boraxobius and S. alvordensis were well corroborated by morphological characters but sequence divergence was only 0.37%. There were three major clades in S. bicolor – a basal S. newarkensis clade in Nevada, an Oregon Lakes S. bicolor clade, and, sister to it, a disjunct S. obesa clade in Nevada and the Oregon Lakes. In the Oregon Lakes, there were two clades within S. bicolor: S. thalassinus was sister to the remaining S. bicolor and there were two clades within S. obesus: S. oregonensis was sister to a "Summer Lake Basin" clade. There was some morphological corroboration for S. oregonensis, but no corroboration for the others. Clades were geographically disjunct or not confined to single basins. The S. oregonensis clade was sister to a Nevada polytomy and historical evidence implicates that at least one population of S. oregonensis in XL Spring was introduced in the late 1800's. Average sequence divergence with the Nevada clade, 0.62 - 0.88%, did not seem to support possible Miocene or Pliocene vicariance scenarios. Elsewhere, the S. thalassinus clade was found outside of Goose Lake in Summer Lake Basin and the "Summer Lake Basin" clade was found in Goose Lake Basin. Clustering of three microsatellite loci did not match cyt b clades, rather, individuals clustered based on sample location, suggesting that the cyt b patterns were due to introgression. In Summer Lake Basin, evidence of poisoning and subsequent transplants was consistent with these observations. These results suggest the presence of three or four tui chub taxa in the Oregon Lakes and Alvord Basin, however translocation and subsequent introgression appear to have been common in many populations, and will prove challenging for taxonomists and conservation managers. / Graduation date: 2013