The main objective of this paper is to elucidate the present status of Plant Genetic Resources (PGRs), their research, and management system in the genebank of Nepal. PGRs for food and agriculture are the biological basis of world food and nutrition security. The remarkable elevation ranging from 60 meter above sea level (masl) to highest summit Mount Everest (8,848 masl) has created huge geographical and climatic variation which harbor enormous plant species in the country. National Agriculture Genetic Resource Center (NAGRC) or ‘Genebank’ currently conserved 11,051 accessions of more than 110 crops species belonging to cereals (5,850), pseudo cereals (1,150), pulses (1,800), oilseeds (185), and vegetables (565) including other crops (1,501) at ex-situ. Diversity mapping, characterization and evaluation of PGRs, duplicates identification, diversity study, pre-breeding and landrace enhancement are the major research works of NAGRC, and its management strategies include conservation method, types, and groupings of PGRs. Characterization, evaluation and tagging of economically important traits in PGRs are now more important for strengthening their pre-breeding and proper utilization. Additionally, strong communication and collaborative network among public, private, community based organizations and international organizations are important for the effective management of PGRs.