Allium incomptum J.A.Kierstead & L.Lindstrand III, sp. nov. (Alliaceae) is described as a new species of Allium from northern California. This new species is most similar to A. yosemitense Eastw., but differs by several features including its shorter pedicels, narrow, blunt tepals, and markedly exserted stamens, contrasted with the longer pedicels, acute tepals, and stamens not or barely exserted in A. yosemitense. The two species have widely disjunct geographic ranges in California, A. incomptum endemic to the eastern Klamath Ranges and A. yosemitense endemic to the central Sierra Nevada. We describe the morphological characters and habitat characteristics for A. incomptum, one in a series of recently discovered vascular plant taxa endemic to the eastern Klamath Ranges.