Jones is a popular surname of English origins. It was first documented in 1279 in Huntingdonshire, England. Its English usage comes from the term son of John in a similar manner to the surname Jonhson. See Johnson surname: http://www.geni.com/surnames/Johnson
In Wales where the name is proportionately much more common it derives from a corruption of Ieuan. It is one of the most common surnames in the Welsh and English speaking parts of the world. Its popularity in Wales stems from the use of Ioan in the Welsh Authorized Version of the Bible. Ioan is used here for Ieuan, the Welsh form of John.