Methods, systems, and computer programs are presented for deduplicating data in a storage device. One method includes an operation for identifying multiple deduplication domains for a storage system. A fingerprint index is created for each deduplication domain, where each data block stored in the storage system is associated with one of the plurality of deduplication domains. The method also includes operations for receiving a first data block the storage system, and for identifying a first deduplication domain from the plurality at of deduplication domains corresponding to the first data block. The first data block is deduplicated within the first deduplication domain utilizing a first fingerprint index associated with the first deduplication domain.