Shin's identity and origins are currently unknown, though Kakashi suggests that he may be a survivor of the Uchiha clan or, more likely, one of Orochimaru's experiments.

Shin Uchiha is the name given to the various individual genetic clones of the original Shin Uchiha, who treats them both as sons and organ donors.
Shin was a former test subject of Orochimaru. After developing a fixation on the Uchiha clan, and more specifically Itachi Uchiha, he took the Uchiha name for himself and severed ties with Orochimaru, taking his "sons" with him. Believing that peace was detrimental to human evolution, Shin began a plot to revive the Akatsuki so that the ensuing conflict would be a catalyst to further his beliefs.
(Source: Naruto Wikia)