Jayaram (1981) reports that at least six other species occur in the north-eastern part of India (Assam to Burma).

Tilak and Hussain (1981) have written a review on the systematics of the Indian members of the genus.

Lepidocephalichthys jonklaasi is distinguished from L. furcatus, L. micropogon, L. manipurensis, and L. goalparensis by rounded/truncated (vs. forked) caudal fin, from L. irrorata and L. kranos by absence of scales on top of head, from L. guntea, L. hasselti, L. tomaculum, L. alkaia, and L. annandalei by broad regularly spaced dark bars (vs. reticulations, spots, or stripe) on caudal fin, from L. thermalis, L. arunachalensis, L. coromandelensis, and L. berdmorei by vertically elongated, dark spots on side that form irregular, thin bars (vs. round spots that sometimes form squares or thin stripe), and from L. lorentzi by thinner, more irregularly spaced dark side bars, dorsal-fin origin anterior (vs. posterior) to pelvic-fin origin, and larger size (to 45 vs. 33 mm SL), (Havird and Page 2010).

They are easily differentiated by body shape and proportions, colour pattern, and form of sexual dimorphism that is unique to L. jonklaasi.

It is not easily confused with L. thermalis owing to its distinctive colour pattern and robust, tubular body.