An ontology is a formal representation of a domain modeling the entities in the domain and their relations. When a domain is represented by multiple ontologies, there is a need for creating mappings among these ontologies in order to facilitate the integration of data annotated with and reasoning across these ontologies. The objective of this paper is to present our experience in aligning two medium-size anatomical ontologies and to reflect on some of the issues and challenges encountered along the way. The anatomical ontologies under investigation are the Adult Mouse Anatomy (MA) and the anatomy subset of the NCI Thesaurus (NCI). We also use the Foundational Model of Anatomy as a reference ontology. We present a hybrid alignment strategy for anatomical entities, combining direct and indirect alignment techniques, both supported by the NLM Anatomy Ontology Alignment System (AOAS). Overall, the hybrid strategy combining direct and indirect alignment techniques identified 1,338 matches between MA and NCI, accounting for about 49% of all MA concepts and 41% of all NCI concepts. 1,007 matches are shared by both alignments, leaving 277 matches specific to the direct alignment and 54 specific to the indirect alignment.