Chaetostoma microps was originally described by Günther (1864) from the 'Andes of Western Ecuador'. Nathan Lujan and collegues redescribed the species in 2015 based largely on specimens collected during a survey they conducted of the Andes of Western Ecuador in 2012.

In a molecular phylogeny generated for that 2015 paper, they found that C. microps from the Napo, Yungantza and Santiago rivers in Ecuador were monophyletic and sister to C. microps from the Huallaga and Marañon rivers in Peru.

Male Ecuadorian C. microps can range from yellow to light blue in coloration, which contrasts with the generally much more plain males from Peru, such as the individuals from the Huancabamba River - compare with Ecuadorian males illustrate below.

Notice also the thickened fleshy cheek pads of this male that obscure the odontodes in ventral view. These are not present in Ecuadorian C. microps.