Most proposed geodynamic models integrate the northern Sierra Nevada and eastern Klamath Mountains in a single island-arc system. New petrological and geochemical data show that the Upper Devonian Sierra Buttes Formation of the northern Sierra Nevada displays important differences from the Lower Devonian Balaklala Formation of the eastern Klamath Mountains. The cale-alkalic affinity of the Sierra Buttes rhyolites (light rare earth element [REE] enriched, low εNd) suggests that they were erupted in a continent-based island arc. In contrast, the Lower Devonian Balaklala low-K tholeiitic rhyolites (light REE depleted, high εNd) are considered to be part of an intraoceanic island-arc sequence. Moreover, the Paleozoic tectogenesis of these two island-arc sequences is different. The Lower Devonian Balaklala rhyolites were affected by the Late Devonian-Early Carboniferous orogeny, whereas the Sierra Buttes Formation is on basement already affected by a pre-Late Devonian deformation. Therefore, at least after Carboniferous time and before Late Triassic time, the eastern Klamath and northeastern Sierra Nevada island arcs cannot be considered lateral counterparts.