ABSTRACT Balancing agricultural needs with the need to protect biodiverse environments presents a challenge to forestry management. An imbalance in resource production and ecosystem regulation often leads to degradation or deforestation such as when excessive cultivation damages forest biodiversity. Lack of information on geospatial biodiversity may hamper forest ecosystems. In particular, this may be an issue in areas where there is a strong need to reassign land to food production. It is essential to identify and protect those parts of the forest that are key to its preservation. This paper presents a strategy for choosing suitable areas for agricultural management based on a geospatial variation of Shannon's vegetation diversity index (SHDI). This index offers a method for selecting areas with low levels of biodiversity and carbon stock accumulation ability, thereby reducing the negative environmental impact of converting forest land to agricultural use. The natural forest ecosystem of the controversial 1997 Ex-Mega Rice Project (EMRP) in Indonesia is used as an example. Results showed that the geospatial pattern of biodiversity can be accurately derived using kriging analysis and then effectively applied to the delineation of agricultural production areas using an ecological threshold of SHDI. A prediction model that integrates a number of species and families and average annual rainfall was developed by principal component regression (PCR) to obtain a geospatial distribution map of biodiversity. Species richness was found to be an appropriate indicator of SHDI and able to assist in the identification of areas for agricultural use and natural forest management.