From a preview of episode 11 of Boruto: Naruto Next Generation, I think something about Mitsuki is going to be revealed.
closed as primarily opinion-based by Ankit Sharma, Dimitri mx♦, Ikaros, Shaymin Gratitude, Danalog Jun 27 '17 at 16:41
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As far as it has been revealed, there is no conclusive proof. In the latest episode (Wednesday June 21st), Mitsuki told Boruto that he knows who is behind the "Ghost Incident", but that is where the episode finished.
He seems to be some sort of "a child" of Orochimaru.
Next episode, it will probably be revealed.
I just read some Boruto manga, and since the manga refers to the future (Chuunin Exams), and Mitsuki is still there, then we can deduce that Mitsuki is not an enemy of Boruto.