A system and method for managing multiple fingerprint tables in a deduplicating storage system. A computer system includes a data storage medium, a first fingerprint table comprising a first plurality of entries, and a second fingerprint table comprising a second plurality of entries. Each of the first plurality of entries and each of the second plurality of entries are configured to store fingerprint related data corresponding to data stored in the data storage medium. A data storage controller is configured to select the first fingerprint table for storage of entries corresponding to data stored in the data storage medium that has been deemed more likely to be successfully deduplicated than other data stored in the data storage medium; and select the second fingerprint table for storage of entries corresponding to data stored in the data storage medium that has been deemed less likely to be successfully deduplicated than other data stored in the data storage medium.