The conservation of habitats and habitat complexes in diverse landscapes is increasingly recognized as a crucial factor in sustaining biodiversity and ecosystems. For the successful management of landscapes, habitat monitoring is necessary, but often small biotopes, e.g. scattered trees, copses, tree rows, hedges, and the transition zones between ecosystems, are ignored. This is important as such small biotopes are recognized as keystone elements in landscape structure for habitat networks. Furthermore, the transition zones between different habitats, often called ecotones, are dynamic and play several functional roles in landscape ecology. This article presents an approach for the extraction of small biotopes and ecotones combining object-based and pixel-based image analysis. Both high-resolution digital elevation data from airborne laser scanning and multi-temporal RapidEye remote-sensing data were used to automatically detect landscape elements and landscape patterns. First, multi-temporal RapidEye images were used to classify the main land-use classes using object-based image analysis. In the second step, a high-resolution digital surface model was integrated with the main classes, and small biotopes and ecotones were delineated by means of pixel-based image analysis. Classification accuracy for main land-use classes is above 92%, and a visual assessment using aerial image and onsite investigation show that the identification results for small biotopes well match reality. The results show the effectiveness of the classification strategy developed and the potential for incorporating the detailed surface mapping in heterogeneous vegetated areas.