Marked chain-order polytopes are convex polytopes constructed from a marked poset. They give a discrete family relating a marked order polytope with a marked chain polytope. In this paper, we consider the Gelfand–Tsetlin poset of type A A , and realize the associated marked chain-order polytopes as Newton–Okounkov bodies of the flag variety. Our realization connects previous realizations of Gelfand–Tsetlin polytopes and Feigin–Fourier–Littelmann–Vinberg polytopes as Newton–Okounkov bodies in a uniform way. As an application, we prove that the flag variety degenerates into the irreducible normal projective toric variety corresponding to a marked chain-order polytope. We also construct a specific basis of an irreducible highest weight representation. The basis is naturally parametrized by the set of lattice points in a marked chain-order polytope.