"French puritan," 1562, from French Huguenot, which according to French sources originally was a political, not a religious, term. The name was applied in 1520s to Genevan partisans opposed to the Duke of Savoy (who joined Geneva to the Swiss Confederation), and on the most likely guess probably it is an alteration of Swiss German Eidgenoss "confederate," from Middle High German eitgenoze, from eit "oath" (from Proto-Germanic *aithaz; see oath) + genoze "comrade," cognate with Old English geneat "comrade, companion," from Proto-Germanic *ga-nautaz "he with whom one shares possessions," thus "comrade," from *nautan "thing of value, possession," from PIE root *neud- "to make use of, enjoy."
Brachet's French etymology dictionary says, "No word has had more said and written about it" and lists seven "chief suggestions" for its origin, the oldest dating to 1560; Scheler's "Dictionary of French Etymology" mentions 16 proposed derivations. The form of the French word probably altered by association with a personal name, a diminutive of Hugues. Hugues Besançon was a leader of the Genevan partisans. In France, applied generally to French Protestants because Geneva was a Calvinist center.