A new variety of Habenaria that is Habenaria pubescens var. nepalensis (Orchidaceae) is described from Nepal, which is similar to typical Habenaria pubescens but can be distinguished by having a much more vigorous stature, a spur equal or longer than the ovary (including pedicel) and deeply bifurcated lateral lobes of the lip. A detailed description of the new variety with illustrations, photographs of dissected parts, key to the allied species and preliminary conservation status are provided. Additionally, we report four new records of orchids for the flora of Nepal.