Great Cipher
Louis XIV's diplomatic cipher, designed by the father-and-son team of Rossignols, which went unread for roughly two centuries.
Antoine Rossignol and his son Bonaventure served the French court in the 1600s and built a nomenclator of around six hundred numeric codes. The clever part was that the numbers stood for syllables rather than letters, and some were traps: one code could mean "ignore the previous group". Anyone hunting for an alphabet found nothing.
Once the Rossignols died the knowledge went with them, and the encrypted letters in the archives became unreadable even to the French. Only in 1893 did the army officer Étienne Bazeries crack it after years of work, when he guessed that a recurring sequence spelled "les ennemis". One of the letters gave him a theory about the identity of the Man in the Iron Mask — a theory historians have yet to buy.