Concerns about the negative effects of declining agricultural biodiversity due to modern agricultural practices and climatic constraints in various parts of the world, including Iran, on the sustainability of agricultural ecosystems are increasingly growing. However, the historical knowledge of temporal and spatial biodiversity is lacking. To identify the value and trend of crop diversity in Iran was used biodiversity indices based on the area under rainfed and irrigated crops and total from 1991 to 2018. The crop species diversity of irrigated cultivation was higher than the rainfed and total cultivations area. The Shannon and Simpson indices had experienced a constant trend, but species richness was increased, which was related to the rise in the area of some species in recent years. The area of wheat and barley had a significant impact on crop diversity so that Shannon diversity was reduced with their dominance. Overall, this study revealed that Iran's agricultural system relies on wheat and barley. We warn that by increasing the area of these crops and the prevalence of monoculture, the probability of damages increased due to external factors such as sudden weather changes or the spread of diseases and the important consequences of which will be instability and production risk in the future.