Ecology is a subject of great debate today among scientists, governments, and the general public. Issues such as global warming and biodiversity require a mutual agreement among different groups of people. Many times these groups are separated by language, political interests, and culture. Environmental Information Systems need to integrate data from different Geographic Information Systems. This may cause problems resulting from the semantic heterogeneity of the source communities. Before this kind of integration can happen among different groups, the concepts that people have about the real world must be explicitly formalized; such an explicit formalization of our mental models is called an ontology. In this paper we discuss two options for structuring such ontologies. First we discuss the use of hierarchies and roles in the structure of geographic ontologies. Second, we discuss some of the fundamental characteristics of ecological ontologies and draw attention to several formal differences between ecological and geographic ontologies. We conclude by identifying some of the important questions that arise in light of our conception of eco-ontologies.