They collect different kinds of royalties.
A Performing Rights Organization (PRO) is responsible for collecting performance royalties on behalf of registered songwriters and publishers when a song is broadcast publicly on television, radio, and other broadcasting systems, played at clubs and restaurants, or otherwise publicly performed.
The Harry Fox Agency is not a PRO, but a mechanical licensing organization. Along with The MLC, Music Reports, and others, it is responsible for licensing and collecting mechanical royalties on the behalf of music publishers in the U.S. These royalties include the recording and reproduction of music streams, CDs, ringtones, and digital downloads.
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