The taxonomy of this species has been debated. At the higher level, some authors place the towhees in the family Fringillidae. Within the group, there has been debate about whether the distinction between this species and the similar canyon towhee ("Melozone fuscus") should be at the specific or subspecific level. The two populations are quite isolated from each other, and molecular genetics seems to have settled the matter in favour of two distinct species for the present. On the other hand, there seems to be little distinction between the northern and Baja Californian populations within "M. crissalis".