A new species, Allium negianum (Amaryllidaceae), belongs to the genus Allium subg. Rhizirideum, sect. Eduardia is described here from the Uttarakhand Himalayan region of India. This taxon grows in Malari region of Niti valley in Chamoli district and Dharma valley of Pithoragarh district, Uttarakhand, India. It is a narrowly distributed species and morphologically more closer to A. przewalskianum Regel but differentiated by its tunic color of bulb, umbel with lax flowers, peduncle length, perigone colour, size and shape and leaf anatomy. Taxonomic delineation and relationship analysis based on nuclear ribosomal Internal Transcribed Spacers (ITS) region indicated that A. negianum is distinct and related to A. przewalskianum. This study provided a comprehensive description and comparison with A. przewalskianum, an identification key and notes on the distribution of the species.