Waikhomia hira was first formally described in 2020 by Unmesh Katwate, Pradeep Kumkar, Rajeev Raghavan and Neelesh Dahanukar with its type locality given as the Kali River near Chandewadi, Kamra, Uttara Kannada District, Karnataka, India at 15°22'13.8"N, 74°24"36.0"E from analtitude of 592 m (1,942 ft).

The specific name, hira is derived from heera the Bengali word for "diamond", an allusion to the small rhomboidal spots along the flanks of tis fish.

[3] Waikhomia hira and its congener W. sahyadriensis,, are distinguished from other related smiliogastrine barbs by the absence of barbels, the rearmost unbranched dorsal fin ray is not serrated and is segmented towards its tip, the pelvic fin are jet black with white tips and the body is marked with between 6 and 8 spots and blotches along the flanks.

W. hira is identified from W. sahyadriensis by having 7 or 8 small, diamond-shaped blotches along the flanks with the lateral line running thropugh them.

[4] Waikhomia hira is endmeic to the northern Western Ghats in Karnataka where it has been recorded from the drainage system of the Kali River.