Abstract. Ontologies undergo changes for reasons such as changes in knowledge, meeting varying application requirements. Thus, for different versions of a considered ontology, it is important to clarify the difference between them. The difference above refers to the logical difference, not syntactic one. Examples of the logical difference include the difference in taxonomy, concept subsumption difference and query difference. These has been well investigated for the lightweight description logic EL because of its tractability and successful application in bio-medical ontologies. Fuzzy EL+ has been put forward and applied in view-based searching in Semantic portals. Thus comes the problem of comparing fuzzy ontologies of different versions and clarifying the difference. In this paper, we define the logical difference of two fuzzy EL+ ontologies. For fuzzy EL+ ontologies of different versions we investigate how to compute the difference in taxonomy and concept subsumption difference. We ...