This chapter reviews the methodologies developed to assess the extent of diversity of PGRFA at species, variety, and genetic level and examines the efforts made at global level in monitoring them at different scales. Efforts have been made to halt the loss of biodiversity (including genetic diversity) by United Nations Organizations (FAO, UNEP, UN) at setting of global targets (second Global Plan of Action on conservation and sustainable use of PGRFA, Aichi Targets and Sustainable Development Goals) and indicators have been established to monitor progress towards them. Yet none of the targets on genetic diversity have been achieved, due to a lack of implementable monitoring system that would allow progress to be accurately monitored. Further research is needed to improve the methodologies for monitoring plant genetic resources, particularly at the varietal and genetic level. The chapter discusses the opportunities and challenges as well as provides recommendations for future conservation and monitoring strategies that may safeguard PGRFA for posterity.