Plants in most populations of Echinocereus bonkerae have radial spines almost pectinately arranged and central spines very short or absent, creating the superficial appearance of E. dasyacanthus, E. pectinatus, or similar species. Formerly, all short-spined plants in central and southern Arizona were treated as E. bonkerae, including unusually short-spined individuals of E. fendleri and E. fasciculatus. Today we recognize that E. bonkerae, E. fendleri, and E. fasciculatus all vary from short-spined to long-spined.
Populations at the lowest altitude for the species have taller stems and unusually long, slender central spines (to 10 cm); they have recently been named Echinocereus apachensis. Such plants were part of the basis for L. D. Benson’s polyphyletic concept (1969, 1982) of E. fasciculatus var. boyce-thompsonii (see 8. E. fasciculatus).
Echinocereus bonkerae is a poorly defined species, frequently lumped with E. fendleri or E. fasciculatus, and it is not always identifiable in the field. Although rib number, blooming season, habitat preference, and, in particular regions, spine length or central spine presence are helpful characteristics, ploidy level is the most objective criterion for distinguishing E. bonkerae from E. fasciculatus. Immature plants of E. bonkerae are like E. fasciculatus and unlike the immature plants of E. fendleri, which are tuberculate with their spines long, few, soft, and often curved or twisted.