The striker had moved into the final year of his original deal at the Keepmoat and rejected an initial offer from Rovers, sparking concerns about his future.
But, after committing his future until 2020, he reiterated what boss Darren Ferguson had been saying since the end of last season - that he always wanted to remain at the club.
“For me I always wanted to stay and like I said a lot last season, my football has come along way with working with the gaffer and his staff,” he told Rovers' official website.
“I am very happy to get the deal done.
"It has taken a little bit longer than I would have liked over the summer, with myself, my agent and the gaffer being away on holiday.
“It's done now and I am really excited about the challenges over the next few years ahead.
"I feel like this club is going places and I want to be a part of that moving forward.”
Marquis netted a divisional best 26-goals in League Two last term as Rovers secured promotion, ensuring he was linked with numerous clubs over the summer.
After proving his quality in the fourth tier, he is looking to do the same in League One in the coming season.
“I want to take the form from last season and take that into this year," Marquis said.
"I want to score as many goals as I can for the team and help the squad get as far up the table as I can.
“The manager has done very well with the players he has brought in, not only here but at previous clubs as well and he plays a good style of attacking football, which as a striker it is a dream to play in because you know that you will get plenty of chances.
“We won a lot of games last season and I want us to take that into this year and if we can take that winning momentum this season with the new additions that we have brought in this season, this club will be on the up.”