When trying to solve interoperability problems between enterprises, the semantic issues are important. To date, they are more and more focused on ontology. This paper presents how to use ontology in the PBMEI method, aimed at solving enterprise interoperability problems in modelling environment. During the elaboration of PBMEI, the necessary ontology information is explicitly specified. Because of two different uses of ontologies, this paper proposes two variants of PBMEI. Finally, this paper concludes with the content of the ontologies required in PBMEI. The ontologies in the PBMEI method PBMEI for an application case are being studied.