The study focuses on the changes of Ortolan Bunting (Emberizia hortulana L.) habitats, which occurred during the last 20 years, and the implications of these changes for the presence of the species population in south-eastern Moravia, Czech Republic. The research was based on aerial photographs and field work. We have identified habitats that were favoured by Ortolan Bunting in the study area on the basis of expert knowledge and by spatial analysis. We found that these habitats experienced statistically significant decline in their area. The decline was steeper in the region where Ortolan Bunting occurred only in the 1990s and was smaller in the region where the bird was present from late 1990s till 2012. However, our analyses did not confirm direct relationship between the habitat changes and the decline of Ortolan Bunting population, i.e. we did not find that decline of favourable habitat significantly affected decline of the species population. The main reasons for the decrease of favourable habitats in the study area are changes in agricultural practices, especially spread of mechanisation that have caused an increase in the size of fields and a drastic reduction of groups of trees and solitary trees. Additionally, widespread grassing of vineyards and other plots as a result of integrated and organic farming contributed to the decrease of favourable habitats. Practices in the form of planting new trees and leaving parts of managed land bare to be used for mitigating the decline of the bird population were discussed.