Botanist Carl Epling considered Salvia microphylla to have three geographical races, though the wide variation still causes confusion today, and there are conceivably more than three races. Adding to the confusion, Salvia microphylla is often mistaken for Salvia greggii, with which it frequently hybridizes. Epling distinguishes between the two by the S. microphylla leaves, which have serrated edges, compared to the narrow, elliptic, and smooth-edged S. greggii leaves — and by a pair of papillae inside the S. microphylla corolla.^[1]

In the U.S. it is sometimes called "Graham's sage", as it has been named Salvia grahamii by George Bentham. It was also named Salvia neurepia byMerritt Lyndon Fernald. Both these botanic names are considered invalid as they are later than microphylla.

There is also confusion between Salvia microphylla and Salvia lemmonii, which was named by Asa Gray. Later, Gray began calling it Salvia microphylla var. wislizenii, considering it to be a variety of S. microphylla, though most taxonomies still consider S. lemmonii to be a unique species.^[1] It has leaves that are .6–1.2 inches (1.5–3 cm) that are furry and sharp-pointed, and flowers that are often vermilion or magenta, with the inflorescence shorter than that of S. microphylla. var. neurepia.^[3]