Input backup data is deduplicated with data of a synthetic backup previously constructed by a deduplication storage system. A synthetic backup is constructed by processing metadata instructions provided by a backup application. Deduplication digests are calculated based on the data of the synthetic backup and the deduplication digests are stored in a digests index. When new backup data is processed, deduplication digests of the new data are calculated and searched in the digests index. Matching digests of previously constructed synthetic backups are located in the digests index. Each of the located matching digest references stored data are included in the synthetic backup, and the stored data is similar to the input backup data. Data matches are found in the input backup data and data in the synthetic backup.