The highly-respected Kinnear began his second spell at Hartsdown Park in April 2011. His side finished 15th last season but began the current campaign among the promotion favourites and are in third place.
Dover occupy the same position in their league despite losing their last five games. They placed their boss Nicky Forster on 'gardening leave' yesterday (Friday) and quickly named Kinnear as his replacement. He had a ten-year spell at Dover from 1985, leading them from the bottom of the Southern League to the Conference.
He also took Margate to the Conference during his first reign there.
Margate's chief executive Cliff Egan said in a statement on margate-fc.com: "Chris has done a great job here and the board would like to thank him for all his hard work.
"At the moment, we are unable to compete with the resources that Dover can offer their manager.
"Chris spent last night thinking about the offer on the table. He came to the conclusion that it would be a great opportunity to test himself at a higher level.
"I know he loves Margate and it wasn’t an easy decision for him, but I understand why he has made it. He leaves the club with our best wishes."
Kinnear's assisant manager, Jake Leberl, is also moving to Dover
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