The semantic web is the web paradigm that represents not general link of documents but semantics and relation of document. In addition it enables software agents to understand semantics of documents. We propose a semantic search based on inference with ontologies, which has the following characteristics. First, our search engine enables retrieval using explicit ontologies to reason though a search keyword is different from that of documents. Second, although the concept of two ontologies does not match exactly, can be found out similar results from a rule based translator and ontological reasoning. Third, our approach enables search engine to increase accuracy and precision by using explicit ontologies to reason about meanings of documents rather than guessing meanings of documents just by keyword. Fourth, domain ontology enables users to use more detailed queries based on ontology-based automated query generator that has search area and accuracy similar to NLP. Fifth, it enables agents to do automated search not only documents with keyword but also user-preferable information and knowledge from ontologies. It can perform search more accurately than current retrieval systems which use query to databases or keyword matching. We demonstrate our system, which use ontologies and inference based on explicit ontologies, can perform better than keyword matching approach .