Francis Godwin (1562–1633) was an English historian, science fiction author, and bishop. Godwin's, Nuncius inanimatus, originally printed in 1629, seems to have been the prototype of John Wilkins's Mercury, or the Secret and Swift Messenger, which appeared in 1641.
"5. The musical cipher. John Wilkins ... in 1641 circulated an anonymous essay entitled Mercury, or the Secret and Swift Messenger. In this little volume ... the author sets forth a method whereby musicians can converse with each other by substituting musical notes for the letters of the alphabet. Two persons understanding the code could converse with each other by merely playing certain notes upon a piano or other instrument.
Musical cryptograms can be involved to an inconceivable point; by certain systems it is possible to take an already existing musical theme and conceal in it a cryptogram without actually changing the composition in any way. The pennants upon the notes may conceal the cipher, or the actual sounds of the notes may be exchanged for syllables of similar sound. This latter method is effective but its scope is somewhat limited.
Several musical compositions by Sir Francis Bacon are still in existence. An examination of them might reveal musical cryptograms, for it is quite certain that Lord Bacon was well acquainted with the manner of their construction." - Manly P. Hall, Secret Teachings of All Ages, p. 562