In a method of and a system for deduplicating backed-up data backup clients create respective backup tables comprising a list of files and respective file types to be backed up. A backup server receives backup tables from the backup clients. The backup server merges the received backup tables to form a merged backup table. The backup server sorts the merged backup table according to file type from a file type yielding a best deduplication ratio to a file type yielding a worst deduplication ratio, thereby forming a sorted backup table. The backup server requests the files listed in the sorted backup table, in order, from the backup clients. The backup server deduplicates files received from the backup clients, in order, using deduplication parameters optimized according to file type. The method calculates an updated deduplication ratio for each deduplicated file type. Examples of deduplication parameters include chunking techniques and hashing techniques.