Ontology alignment is an important task for information integration systems that can make different resources described by various and heterogeneous ontologies interoperate. However very large ontologies have been built in some domains like medicine or agronomy and the challenge is now in scaling up alignment techniques that often perform complex tasks. In this paper, we propose two partitioning methods which have been designed to take the alignment objective into account in the partitioning process as soon as possible. These methods transform two ontologies to be aligned into two sets of blocks of a limited size. Furthermore, elements of the two ontologies that might be aligned are grouped in a minimal set of blocks that will be then really compared. Results of experiments performed by the two methods on various pairs of ontologies are convincing.