Chefs Jon Rotheram and Tom Harris’s Hackney pub, which opened just last year, marks the first time the award has gone to a pub in the capital.
Rebecca Burr, editor of the Michelin Guide, said: “The Marksman cleverly combines a place to drink with new era pub food."
She added: “One of the things we love about it is that it’s a proper neighbourhood pub first and foremost, with a cosy, traditional bar in which to enjoy a pint of local ale or a bottle of craft beer.”
Dishes on offer at the pub include bacon buns with burnt apple ketchup; devilled sardines and fennel; treacle-cured Tamworth pork belly with white cabbage and beer mustard; and partridge with pumpkin and pickled walnut.
Desserts include plum sherbert; buttermilk ice cream with blueberries and oats; and brown butter and honey tart.
Last year, the award went to Michelin-starred Gloucestershire freehouse the Butchers Arms, Eldersfield, which is run by chef-patron James Winter.
Michelin released the 2017 edition of its Eating Out in Pubs Guide today (28 October), which recommends the best pubs for dining across the UK.
Burr said: “We are increasingly witnessing how pubs can provide a platform for young chefs to start their own businesses, and how inventive these chefs can be, particularly when it comes to the sourcing of their ingredients.
“The quality of cooking in some of these pubs certainly rivals that of restaurants.”
Both pubs ranked in 2016’s Top 50 Gastropubs, coming in respectively in 22nd and 29th place.