It's not really clear the origin of the name Flamenco for this music genre and it's relatively a recent name, XIX century, for a kind of music that existed long before. One hipótesis is the music came from Flanders during the reign of Carlos V. I prefer the simpler version stating that Flamenco is the word used in Andalucía to refer to Gypsy people; this genre and much of the southern Spain culture is clearly influenced by gypsy culture.

Etymology

Borrowed from Dutch Vlaming.

https://en.wiktionary.org/wiki/flamenco#Spanish