Experts from the Rome-based organisation warned that the loss of biodiversity will have a major impact on humankind's ability to feed itself in the future as the global population rises to nine billion by 2050.
"There are thousands of wild crop relatives that... hold genetic secrets that enable them to resist heat, droughts, salinity, floods and pests," FAO director general Jacques Diouf was quoted in the report as saying.
"Increasing the sustainable use of plant diversity could be the main key for addressing risks to genetic resources for agriculture," he said.
The report estimated that 75 percent of crop diversity was lost between 1900 and 2000 and called for "special efforts to conserve and use" both cultivated plants and their "wild" relatives, especially in developing countries.
Fifty percent of the increase in crop yields in recent years has come from new seed varieties, the report said.
FAO experts pointed in particular to the success of New Rice for Africa (NERICA), a cultivator of new types of rice suited to drylands that has transformed local economies in several parts of Africa.
The FAO's second report in 12 years on the state of the world's plant genetic resources covers a range of topics from gene bank collections to the effects of climate change.
The study predicts that as much as 22 percent of the wild relatives of important food crops of peanut, potato and beans will disappear by 2050 because of the changing climate.
The United Nations has named 2010 as the International Year of Biodiversity.