Juvenile plants of Chimarrhis hookeri have more robust leaves and stipules than found on reproductive stems. The juvenile plants are sometimes similar to sterile juvenile plants of Semaphyllanthe megistantha, with stipules that are not twisted.
Chimarrhis hookeri was separated by Delprete (1999) from Chimarrhis glabriflora, based on several vegetative characters and a pubescent vs. glabrous disk. The features that separated these ae variable, however, and additional collections document the variation as continuous. The disks vary from glabrous to minutely puberulous to densely pubescent; these last two conditions were included in Chimarrhis hookeri while the first distinguished Chimarrhis glabriflora. Sterile specimens of these two species cannot be separated, and material annotated by Delprete does not all correspond to his diagnostic features; see the page for Chimarrhis glabriflora for more details. These names are not separable morphologically, an are synonymized here. Chimarrhis hookeri is also similar to Chimarrhis microcarpa, Chimarrhis speciosa, and Chimarrhis parviflora.