Plants from the eastern and southern parts of the range of Aquilegia desertorum have usually been considered a distinct species, A . triternata , mainly because of their longer sepals and petal blades (sepals narrowly ovate to lanceolate, 12-20 × 4-8 mm, apex acuminate, petal blades 6-12 mm in A . triternata versus sepals ovate or elliptic-ovate, 7-13 × 3-6 mm, apex obtuse or acute, petal blades 3-5 mm in A . desertorum in the strict sense). These sepal and petal types intergrade over much of central Arizona, however, and other characteristics supposedly diagnostic for A . triternata (leaves not glaucous, 3×-ternately compound) are scarcely correlated with the flower characteristics or with one another.
The Navaho-Kayenta used Aquilegia desertorum as an aid in ceremonies (D. E. Moerman 1986).