Human activities often cause changes and homogenization in landscape structure. To investigate the impact of changing cultivation systems on structural and functional aspects of a tropical agroforestry system, we developed satellite based land cover maps of the La Gamba area in southwestern Costa Rica and refined them by mapping fine-scale linear landscape elements. Performing a landscape pattern analysis, we compared eight sections of the study area by landscape metrics. Furthermore we performed a Morphological spatial pattern analysis (MSPA) for hypothetical non-forest, forest generalist and forest specialist species, and compared the current situation to a possible future scenario with double the area covered by oil palm plantations after a virtual conversion of other agricultural patches. The heterogeneous rural sections clearly differed from the homogeneous forests and especially pasture-dominated rural sections included many diverse, small and elongated patches, many linear landscape elements but few big plantations. According to the scenario with double the area covered by oil palm plantations, non-forest species lost large parts of their habitat, while forest species mainly lost corridors. The protection of natural landscape elements that support wildlife movement between forest areas is of major importance, particularly as the globally increasing cultivation of oil palm is significantly altering many tropical land mosaics, including the countryside of La Gamba. We propose the establishment of eight least cost path corridor routes in the study area to make the agricultural area pervious for wildlife.