[5][6][8] Considerable taxonomic uncertainty surrounds the northern subspecies caniceps, sybilla and marica of the spotted giant flying squirrel.

[9] Another study that compared north Vietnam specimens (either sybilla or marica based on appearance and location) with P. elegans also revealed a relatively deep genetic split between them.

[4] A secondary problem is related to certain Chinese and Nepali populations, by some authorities recognize as the subspecies clarkei and gorkhali,[8][12] but others consider both as synonyms of caniceps.

[10] Additionally, populations in the Chinese provinces of Gansu, Guangxi, Hubei, Hunan and Shaanxi appear to belong to two undescribed taxa.

[4][15] P. e. banksi of highlands of northern Borneo is similar, except that its upper head, nape and back are black, resulting in a clear contrast with the rich rufous-brown flanks and tail base.

P. e. marica from Mainland Southeast Asia (except the Thai-Malay Peninsula) and southern Yunnan and westernmost Guangxi in China is lighter brown above than P. e. punctata and has less white spots that mostly are distributed on the top of the head to the central back.

P. e. sybilla of northern Myanmar, southern Sichuan and Yunnan in China and easternmost Arunachal Pradesh in India is orangish-brown or reddish-brown above with a slightly more grey-brown back that completely lacks white spots.