The Downingia yina species complex (Campanulaceae), centered in northern California and southern Oregon, currently contains three morphologically distinguished species: D. yina, D. elegans, and D. bacigalupii. This complex of species is notable for high levels of morphological and cytological variation, with chromosome counts of n  =  6, 8, 10, and 12. Molecular evidence suggests three main clades within this complex, corresponding more with cytological variation than with morphological variation. Additionally, the molecular evidence suggests a phylogeographic pattern associated with the Cascade Ranges, where members of the clade characterized by chromosome counts of n  =  6, 8, and 10 are distributed primarily to the west of the Cascades while members of the clade characterized by chromosome counts of n  =  12 are distributed primarily to the east. A third clade characterized by n  =  10 is localized in the Lake of the Woods region of southern Oregon. Evidence from morphological, cytological, interfertility, and molecular data was used to re-examine the delimitation of species within this complex. Downingia elegans and D. bacigalupii are maintained, while D. yina is split into three morphologically cryptic species (D. yina, D. willamettensis, D. pulcherrima) that do not form a clade.