Segmented fingerprint datastore and scaling a fingerprint datastore in de-duplication environments

A storage server is coupled to a storage device that stores data blocks, and generates a fingerprint for each data block stored on the storage device. The storage server creates a master datastore and a plurality of datastore segments. The master datastore comprises an entry for each data block that is written to the storage device and a datastore segment comprises an entry for a new data block or a modified data block that is subsequently written to the storage device. The storage server merges the entries in the datastore segments with the entries in the master datastore in memory to free duplicate data blocks in the storage device. The storage server overwrites the master datastore with the entries in the plurality of datastore segments and the entries in the master datastore to create an updated master datastore in response to detecting that the number of datastore segments meets a threshold.