New regional mapping documents that a thick quartzite sequence in the Lemhi subbasin of the Belt-Purcell basin lies near the top of the Mesoproterozoic stratigraphic column, and that two finer-grained units have been miscorrelated. This observation requires reassessment of the subbasin's stratigraphy, which we present here. Determination of the relationships between the stratigraphic units of the Lemhi Range and Salmon River and Beaverhead Mountains and better-known Belt Supergroup units to the north has been hampered by miscorrelation of this upper quartzite sequence with older strata, and by miscorrelation of the type Apple Creek Formation with a similar but stratigraphically lower unit. The base of the upper quartzite sequence includes the Swauger and Lawson Creek Formations, which are the highest units previously identified in the Lemhi subbasin. This sequence continues upward through quartzite units described here that underlie or comprise lateral equivalents of the type Apple Creek Formation in the Lemhi Range. The spatial distribution of these quartzite units extends the Lemhi subbasin farther east and north in Montana and northwest in Idaho. The complete stratigraphy reflects the stratigraphic separation of the two “Apple Creeks” and expands the type Apple Creek Formation to accommodate the quartzite units into the regional Mesoproterozoic stratigraphy. Our proposed correlation of the thick upper quartzite sequence with the Bonner Formation and higher units of the Missoula Group in the main part of the Belt basin requires that subsidence of the Lemhi subbasin was significantly faster than that of the main part of the Belt basin during deposition of the upper Missoula Group. Therefore, the two parts of the Belt basin were distinct tectonically, although they shared common sediment sources.