A media identification system generates reference fingerprints for known media samples and stores the reference fingerprints in a reference database. The media identification system uses the reference fingerprints to match a fingerprint generated from an unknown media sample to identify that unknown sample. When storing new reference fingerprints in the reference database, partitions of the database are selected to balance the search loads on the database when it is used by the media identification system. For example, the selected partitions may be determined based at least in part on the access rates of the partitions by the media identification system. New reference fingerprints will tend to be placed in partitions that have relatively lower access rates that the other partitions, which will tend to balance the search loads on the partitions by the media identification system.