Amino acid geochronology based on fossil molluscs provides a useful approach to determining the Quaternary history of Great Basin lakes. The Lahontan basin, Nevada, and the Chewaucan basin, Oregon, in the northwest corner of the Great Basin, both contained lakes during the Quaternary. The aim of this study is to improve the Quaternary geochronology in these two basins by measuring time-dependent changes in amino acids preserved in fossil molluscan shells. The abundance of D-alloisoleucine relative to Lisoleucine (All) characterizes the extent of racemization, which increases with age and Ul forms the basis of relative and correlated ages. An age-calibration curve for Vorticifex was developed using All ratios in shells from layers with radiocarbon-dated shells and with one thermoluminescence date in the Chewaucan basin. The All ratios from non-dated deposits were assigned ages from this calibration curve. The All ratios in 77 samples (-350 shells) of mainly Vorticifex were analyzed to improve the lake chronology in the Lahontan and Chewaucan basins. From the stratigraphic position, All ratios in the shells, and previously published radiometric ages, at least five and possibly six lake cycles were inferred in the Lahontan basin for the Quaternary period. Shells with highest All ratios ( -0.8) might correlate with the Rye Patch Alloformation, named for deep-lake sediments deposited in the Lahontan basin -630 ka. The next younger lake deposits are ascribed to the Eetza Alloformation. On the basis of the amino acid data, two and possibly three distinct lake expansions took place during the Eetza lacustrine episode, which lasted from -385 to 145 ka. Deposits of the Sehoo Alloformation ( -35 to 12 ka) can be differentiated from older deposits on the basis of All ratios in mollusc shells. Finally, a few shells with low All ratios near Pyramid Lake may indicate a minor lake expansion during the Holocene. Only two lake cycles were inferred from the amino acid data in the Chewaucan basin for the Quaternary period. Shells with the highest ratios correlated with the Eetza Alloformation and the shells with lowest ratios correlate with the Sehoo Alloformation. The amino acid data suggest that Lake Lahontan and Lake Bonneville experienced similar lake-level histories during the past -660 ka. The Sehoo Alloformation in the Lahontan basin broadly correlates with Bonneville Alloformation in the Bonneville basin based on All ratios and radiocarbon dates. The late and early aminozones within the Eetza Alloformation might correlate, respectively, with the Little Valley and Pokes Point Alloformations in the Bonneville basin.