One of the major questions among ecologist has been which factors contribute to determining biodiversity. Compartmentalization of the community and interaction diversity are thought to support species coexistence. These factors may be related. For example, given a set of species in a continuous habitat with different environment, if communities compartmentalize depending on environment, and if the relationship between the species is different in each compartment, then overall interaction diversity may increase. In order to discuss the possibility of this hypothesis, it is first necessary to demonstrate the existence of compartmentalization. This study was conducted to examine the structure of the food-web of lizard communities focusing on compartmentalization. 10 species of lizards were used in a continuous habitat with different degree of human disturbance in a dry forest of Madagascar. Stable isotope ratios of carbon and nitrogen were used to examine compartmentalization and trophic position of lizards. Results showed that the isotopic ratios of lizards dramatically shift along with the environmental gradient, suggesting compartmentalization of the communities.