Gulls boss Paul Buckle, who coached Ellis as a 16-year-old at Exeter, told the Herald Express: "You need four quality centre-halves if you are going to have any chance of doing anything.
"I told Colin (chief executive Colin Lee) that I really wanted the boy, and he's negotiated the deal with Bolton.
"I said from Day One that Mark can go on to play higher. He's got a bright future ahead of him.
"He's shown what he can do already, and now he's in competition with the other three centre-halves here.
"We are going to need them all, with the demands that the winter months bring."