Fragmentation of natural habitats is currently regarded as one of the most serious reasons of species extinction. The influences of natural habitat fragmentation to wildlife species increase with expansion of urban areas and network of roads. The purpose of this study is to quantify and evaluate the fragmentation of thermophilous oak forests on loess in the Trnava upland (southwest Slovakia) listed among prior biotopes according to EC Habitat Directive 92/43/EEC. Changes of the 17 forest remnants in agricultural landscapes have been reconstructed since 1919 (for three of them since 1747) on the base of historical and recent maps and data from literature sources. The fragmentation process is evaluated according to the characteristic attributes of: area size, number of fragments, area categories, the distance from the other remnants, isolation and connectivity. As the results indicate the process of woods fragmentation and isolation on the Trnava upland is not static, but is still continuing. The area of the seventeen investigated woods decreased during 20th century about 1300 ha.