Crop diversity or crop biodiversity is the variety and variability of crops, plants used in agriculture, including their genetic and phenotypic characteristics. It is a subset of a specific element of agricultural biodiversity. Over the past 50 years, there has been a major decline in two components of crop diversity; genetic diversity within each crop and the number of species commonly grown.

Crop diversity loss threatens global food security, as the world's human population depends on a diminishing number of varieties of a diminishing number of crop species. Crops are increasingly grown in monoculture, meaning that if, as in the historic Great Famine of Ireland, a single disease overcomes a variety's resistance, it may destroy an entire harvest, or as in the case of the 'Gros Michel' banana, may cause the commercial extinction of an entire variety. With the help of seed banks, international organizations are working to preserve crop diversity.

The loss of biodiversity is considered one of today's most serious environmental concerns by the Food and Agriculture Organization. If current trends persist, as many as half of all plant species could face extinction. Some 6% of wild relatives of cereal crops such as wheat, maize, rice, and sorghum are under threat, as are 18% of legumes (Fabaceae), the wild relatives of beans, peas and lentils, and 13% of species within the botanical family (Solanaceae) that includes potato, tomato, eggplant (aubergine), and peppers (Capsicum).

Within-crop diversity, a specific crop can result from various growing conditions, for example a crop growing in nutrient-poor soil is likely to have stunted growth than a crop growing in more fertile soil. The availability of water, soil pH level, and temperature similarly influence crop growth.

In addition, diversity of a harvested plant can be the result of genetic differences: a crop may have genes conferring early maturity or disease resistance. Modern plant breeders develop new crop varieties to meet specific conditions. A new variety might, for example, be higher yielding, more disease resistant or have a longer shelf life than the varieties from which it was bred. The practical use of crop diversity goes back to early agricultural methods of crop rotation and fallow fields, where planting and harvesting one type of crop on a plot of land one year, and planting a different crop on that same plot the next year. This takes advantage of differences in a plant's nutrient needs, but more importantly reduces the buildup of pathogens.

Both farmers and scientists must continually draw on the irreplaceable resource of genetic diversity to ensure productive harvests. While genetic variability provides farmers with plants that have a higher resilience to pests and diseases and allows scientists access to a more diverse genome than can be found in highly selected crops. The breeding of high performing crops steadily reduces genetic diversity as desirable traits are selected, and undesirable traits are removed. Farmers can increase within-crop diversity to some extent by planting mixtures of crop varieties.

Agricultural ecosystems function effectively as self-regulating systems provided they have sufficient biodiversity of plants and animals. Apart from producing food, fuel, and fibre, agroecosystem functions include recycling nutrients, maintaining soil fertility, regulating microclimate, regulating water flow, controlling pests, and detoxification of waste products.

However, modern agriculture seriously reduces biodiversity. Traditional systems maintain diversity within a crop species, such as in the Andes mountains where up to 50 varieties of potato are grown. Strategies to raise genetic diversity can involve planting mixtures of crop varieties.