1. A method for identifying data in a data deduplication system, by a processor device, comprising: 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, for data writes to a given one of the metadata regions, the direct inter-region fingerprint lookup first searches an index of the fingerprints within the given one of the metadata regions, and subsequently searches a separate yet supplemental central fingerprint index if the fingerprint matches are not found within the given one of the metadata regions, the central fingerprint index indicating in which of the plurality of metadata regions the fingerprints reside; and deduplicating the identified duplicate data using the identified fingerprint matches from at least one of the index within the given one of the metadata regions and the central fingerprint index.