Abstract The taxonomy of the genus Juga (Semisulcospiridae), as in many freshwater mollusks, poses several challenges. Only a few species have been studied genetically or anatomically. We analyzed a portion of the cox1 gene for 103 specimens, emphasizing the upper Sacramento – Pit system but including all recognizable named species and subspecies from across the geographic range. The rrnL gene was also sequenced for 35 specimens and showed similar patterns, but was less informative. None of the three extant subgenera appear monophyletic and additional clades of similar rank exist. Several currently recognized taxa such as Juga silicula, Juga nigrina, Juga hemphilli, Juga bulbosa , and Juga acutifilosa are polyphyletic. In contrast to previous classifications, the clades found in our study correspond closely to geography. Some geographically and genetically distinctive populations do not fit in any named species.