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With the rapid growth of semantic Web, more and more semantic Web data are generated and widely used. Efficient search and management of the semantic Web data is becoming a very important issue. In this paper, we present semantic Web data indexing scheme over a fully decentralized P2P network. Ontological knowledge is decomposed into atomic elements and then indexed with a distributed hash table (DHT) overlay. Ontology reasoning, integration, and searching are all based on the index. A complex SPARQL query can be evaluated by performing relational operations such as select, project, and join on combinations of the atoms. A set of experiments have been made to show the effectiveness and efficiency of the proposed indexing scheme.