The paleogeographic position of rocks of the northern Sierra Nevada relative to North America has long been the topic of debate. A detailed study of the Lakes Basin region of the northern Sierra Nevada substantiates that the Shoo Fly Complex, of early Paleozoic age, was folded and unconformably overlain by an island-arc sequence in late Paleozoic time. Microfossils recovered during the study represent the first in situ fauna ever collected from the Shoo Fly Complex and provide an Ordovician-Silurian lower limit on the early deformation. Late Jurassic (Nevadan) deformation strongly affected all rocks in the region. Regional considerations suggest that mid-Paleozoic deformation may have been widespread in the Sierra Nevada and could indicate an early phase of an eastward-prograding suture that ultimately resulted in emplacement of the Roberts Mountain allochthon of the Great Basin.