Ontology alignment is regarded as one of the core tasks in many Web services. It is concerned with finding the correspondences between separate ontologies by identifying concepts with the same or similar semantics in order to resolve semantic heterogeneity between them. Existing ontology alignment techniques are tailored towards today’s ontology languages, which are not capable of representing and reasoning with uncertain or incomplete information. It is expected, however, that future Semantic Web services will rely on the development and use of proper domain ontologies. Alignment of such ontologies goes beyond standard concept matching, and requires non-standard logic processing. In this paper, we present an alignment technique utilizing an alternative, rule-based representation, which provides a uniform framework for representing and mapping heterogeneous ontologies. To justify and illustrate our research, we describe an example application scenario.