[3] There are two subspecies: the western P. n. nobilis (Nepal, Sikkim and West Bengal) and eastern P. n. singhei (Bhutan and Arunachal Pradesh).

[6][9] The shoulders of the Bhutan giant flying squirrel are yellowish-buff or orange-buff and this colour extends along the flanks, bordering and clearly contrasting with the rich chestnut-brown or maroon-brown back ("saddle").

[2][3] In some individuals, the light colour of the shoulders and flanks extends even further to the posterior and join on the lowermost back, almost completely encircling the dark saddle.

[6] There is a distinct pale fulvous or orange-buff band/patch on the crown (making the dark top of the head appear rather like a bandit mask),[3][10] although this band/patch occasionally is poorly defined or entirely absent in P. n.

[9] Most P. n. nobilis have a distinct buff stripe along the mid-back (dividing the dark "saddle"), but it is occasionally incomplete or even absent.

[8][9] The underside of the Bhutan giant flying squirrel is uniformly coloured light pale rufous, salmon-buff or ochre, and the patagium is orange-rufous.

This was repeated by others, even authorities with access to museum specimens showing that neither colour pattern is restricted to a specific season.

[8][9] In addition to its smaller average size (although its tail may be longer) and differences in the skull, the Hodgson's giant flying squirrel has large yellowish-buff shoulder patches that contrast with the deep russet or chestnut flanks, lacks a light stripe along the mid-back, and the light patch on the crown—if present at all—only consists of a spot that occasionally forms a streak.