It is well known that the Einstein equation on a Riemannian flag manifold (G/K, g) reduces to an algebraic system if g is a G-invariant metric. In this paper we obtain explicitly new invariant Einstein metrics on generalized flag manifolds of Sp(n) and SO(2n); and we compute the Einstein system for generalized flag manifolds of type Sp(n). We also consider the isometric problem for these Einstein metrics.