1. A computer-implemented method of identifying a source of media using a fingerprint of the media, comprising: performing the following actions using at least one computer: identifying a plurality of segments arranged to form said media; generating the fingerprint of the media including a representative master key (RIMK) from the arrangement of the plurality of segments, wherein the fingerprint indicates a source file of the media for each segment to be included in a fingerprinted file, and wherein the RMK comprises a first listing of master identifiers corresponding to the plurality of segments, each master identifier of the first listing of master identifiers identifying a source master of each segment of the plurality of segments; receiving a listing of fingerprints, each fingerprint of the listing of fingerprints having a corresponding identifier that identifies the source of said media, said each fingerprint also including a second listing of master identifiers; and comparing the first listing of master identifiers in the RMK to the second listing of master identifiers in said each fingerprint in the listing of fingerprints to identify the source; generating the fingerprinted file by selecting segments from a plurality of source files according to the fingerprint of said media, and including the selected segments in the fingerprinted file, wherein the fingerprinted file includes at least two segments that are from different source files and at least one is marked differently from the other source files.