The former Pompey striker will join Max Melbourne in leaving the Imps after their exits were confirmed by the club via their retained list.
It means the 29-year-old – who has already been linked with Charlton – moves on from Sincil Bank after just five months, following his switch from the Blues in January.
He departs with five goals in 20 games for Lincoln, who finished the season in 17th position.
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Prior to his move to Michael Appleton’s then side, Marquis scored four goals in 19 league games for Pompey this season.
He departed PO4 will a goal return of 36 from 121 appearances during his second spell at the club.
The former Doncaster Rovers ace started life at the Imps with a bang, scoring in each of his opening three games for his new side.
Yet he ended the campaign without a goal in 11 appearances.
Now a free agent, the former Millwall and Doncaster Rovers front man will be keen to nail down his next club.
News of a move to manageress Charlton has been brewing, but it’s understood, at this stage, he remains an option the south London side are considering.
The Addicks parted company with manager Johnnie Jackson following their disappointing 13th-placed finish in the League One table.
Since then Charlton have also revealed their retained list, with striker Conor Washington – their second-highest goalscorer this season – Adam Matthews, Chris Gunter, Ben Watson, Pape Souare and Stephen Henderson all departing.