The genetic resources of Allium in India constitute cultivated species, onion (Allium cepa L.), garlic (A. sativum L.), leek (A. porrum L.), shallot (A. ascalonicum L.), and chives (A. schoenoprasum L.) besides several less-known species reported from the north-western Himalayan region of India. About 40–45 species of Allium occur as cultivated and wild taxa from temperate to alpine regions of the Indian Himalaya and tropical areas that are broadly distributed in different agro-ecological regions. Some of the less-known cultivated species—A. porrum/ ampeloprasum var. ampeloprasum, A. chinense, and A. tuberosum—are grown as backyard cultigens in tribal-dominated tracts of Indian Himalaya and north eastern hill region. A. tuberosum has grown its regional value for large-scale cultivation in north-eastern hills. Whereas regional importance of A. stracheyi, A. wallichi, and A. humile in Kumaon and Garhwal Hiamlayan region as spice and condiments and vegetable, A. przewalskianum and A. schoenoprasum as flavor, and as salads in Leh and Lahaul and Spiti regions, A. hookeri and A. chinense as vegetable/pickle in North Eastern India is confined to local levels. Himalayan species, A. roylei a potential source used for powdery mildew and leaf blight resistance to cultivated onion, A. cepa and A. stracheyi an “endangered” species in wild in high altitude areas of Uttarakhand are valuable genetic resources. The data on global germplasm holdings of Allium spp. at main centers suggest that the onion germplasm has been collected extensively, but germplasm of its wild relatives is only poorly represented in worldwide genebanks. ICAR-National Bureau of Plant Genetic Resources has augmented Allium germplasm of a total of 5,004 accessions following the standard guidelines and through geo-referencing. Status of indigenous collections identified gaps and areas for germplasm collection and conservation. Among the less-known minor cultivated taxa, namely A. ampeloprasum, A. cepa var. aggregatum, A. cepa var. viviparum, A. chinense, A. fistulosum, A. hookeri, A. porrum, A. proliferum, and A. tuberosum, were well collected from different states of the country. The most potential wild species, A. roylei, a crop wild relatives (CWR) of Allium, is poorly represented. Allium seeds have short longevity, and therefore, conservation protocols for seed viability have been worked out at the NGB (National Gene Bank). The germplasm is held at seed genebank, in-vitro repository, cryo genebank, and field genebank at ICAR-NBPGR, India, besides holings at ICAR-Directorate of Onion and Garlic Research (ICAR-DOGR), Pune, Maharashtra. Poor representation of wild species in collection may be attributed to various reasons like niche-specificity, lack of ex-situ conservation protocols, rapid loss of viability, and poor performance/non-suitability to climatic conditions of field gene bank at Pune and Bhowali. Conservation methods (in parenthesis) were suggested: (a) for most common species producing seeds in enough quantity (seed genebank or in vitro method; (b) for less-common species (seed genebank and in vitro methods); and (c) for species having poor seed production or reported to be endemic, rare/threatened, etc. (seed genebank, in vitro, and field genebank).