1. A method for identifying data in a data deduplication system, by a processor device, comprising: efficiently identifying duplicate data in the data deduplication system by identifying fingerprint matches using a direct inter-region fingerprint lookup to search for the fingerprint matches in at least one of a plurality of metadata regions, the metadata regions each comprising a certain area of user space swapped in and out of memory and containing fingerprints for all data chunks written to the certain area of user space, wherein the direct inter-region fingerprint lookup searches an index of the fingerprints within the given one of the metadata regions and is separate from yet supplements a central fingerprint index; and deduplicating the identified duplicate data using the identified fingerprint matches.