Today’s market evolution and high volatility of business requirements put an increasing emphasis on the ability for systems to accommodate the changes required by new organizational needs while maintaining security objectives satisfiability. This is all the more true in case of collaboration and interoperability between different organizations and thus between their information systems. Ontology mapping has been used for interoperability and several mapping systems have evolved to support the same. Usual solutions do not take care of security. That is almost all systems do a mapping of ontologies which are unsecured. We have developed a system for mapping secured ontologies using graph similarity concept. Here we give no importance to the strings that describe ontology concepts, properties etc. Because these strings may be encrypted in the secured ontology. Instead we use the pure graphical structure to determine mapping between various concepts of given two secured ontologies. The paper also gives the measure of accuracy of experiment in a tabular form in terms of precision, recall and F-measure.