It belongs to the large subgenus Rabdophorus which might warrant recognition as a distinct genus. In this group, its relationships are doubtful; it seems related to the "raccoon-masked" group including the black butterflyfish (C. flavirostris), diagonal butterflyfish (C. fasciatus), Philippine butterflyfish (C. adiergastos) and the raccoon butterflyfish (C. lunula). Its color and pattern is entirely different from these, but it shares the robust habitus and bold habits.[3][4]
The mailed butterflyfish (C. reticulatus) is a near-match of C. collare in appearance, save for a less brown hue and light blue instead of red in its black-based tail. These two are widely sympatric in the western Pacific. But DNA sequence and osteology data overwhelmingly agree that C. reticulatus belongs to the subgenus called "Citharoedus" (a name preoccupied by a mollusc genus). This contains fish like the scrawled butterflyfish (C. meyeri), similar in shape and size but with a "finger-painted" pattern of a few prominent and uneven lines on light silvery background.[5][3][4]
If Rabdophorus were to be considered a distinct genus, "Citharoedus" would not be included in it but placed with the subgenera Lepidochaetodon or Megaprotodon. Thus, the red-tailed and mailed butterflyfishes probably represent a case of convergent evolution and perhaps mimicry. What selection forces were responsible for the striking similarity between two rather unrelated Chaetodon is not known.[3][4]
The highly anomalous 12S rRNA mtDNA sequence found in this species in one 2007 study seems to be due to a laboratory error; in another study a 12S rRNA sequence agreeing with the general pattern of mtDNA evolution in Rabdophorus was found.[3][4]