Allium sanbornii is a member of the Sanbornii alliance which is characterized by prominent ovarian crests and a single terete leaf. Because of inadequate material, previous investigators have confused species limits and lumped together taxa that are not conspecific. This investigation included herbarium and field studies and determined that previously ignored characters, such as the relative lengths of the inner and outer perianth segments, general attitude of the perianth segments and texture of the outer bulb coat, were useful in delimiting relationships within the complex. Based on these findings Allium sahbornii consists of two geographic variants: A. sahbornii var. sanbornii and A. sanbornii var. congdonii. The two other currently recognized varieties are elevated to specific status as A. jepsonii and A. tuolumnense.