A key requirement for systematic conservation planning is the availability of good quality and comparable data about the biodiversity. However, for many highly diverse countries, this information is not available. Here we present the methodology and the results of the three-part construction of a conservation planning database in Colombia: (1) the actual distribution of the ecosystems; (2) their original-potential distribution, which is important to calculate fixed targets for conservation; and (3) the chorological types, which are groups of spatial related ecosystems that account for biodiversity process that operate at larger scales. The procedure consists of integrating the results of the interpretation of satellite images, and the construction of ecological diagrams and biogeographical regions. The limits of the original-potential ecosystems in the transformed landscapes can either still be seen on the images or are reconstructed on the base of the information from the ecological diagrams. The chorological types are constructed by clustering of ecosystems on the base of the shared boundary length. The implementation for Colombia resulted in maps of 337 ecosystems and 63 chorological types. This database was successfully used for the identification of the priorities for conservation.