Ontologies reflect their creators’ view of the domain at hand and are thus subjective. For specific applications it may be necessary to combine several of these ontologies into a more comprehensive domain model by merging them. However, due to the subjective nature of the source ontologies, this can result in inconsistencies. Handling these inconsistencies is a challenging task even for modestly sized ontologies. Therefore, in this paper, we propose a Subjective Logic based approach to cope with inconsistencies originating in the ontology merging process. We formulate subjective opinions about the inconsistency causing axioms based on several pieces of evidence such as provenance information and structural relevance by utilizing consensus and conditional deduction operators. This allows creating an environment that supports handling of these inconsistencies. It provides the necessary mechanisms to capture the subjective opinion of different communities represented by the input ontologies on the trustworthiness of each axiom in the merged ontology and identifies the least trustworthy axioms. It suggests remedies of the inconsistencies, e.g. deleting or rewriting axioms, to the user. Our experimental results show that with this approach it is possible to overcome the inconsistency problem in ontology merging and that the approach is feasible and effective.