For a Hermitian Lie group G of tube type we find the contribution of the holomorphic discrete series to the Plancherel decomposition of the Whittaker space L2(G/N,ψ), where N is the unipotent radical of the Siegel parabolic subgroup and ψ is a certain non-degenerate unitary character on N. The holomorphic discrete series embeddings are constructed in terms of generalized Whittaker vectors for which we find explicit formulas in the bounded domain realization, the tube domain realization and the L2-model of the holomorphic discrete series. Although L2(G/N,ψ) does not have finite multiplicities in general, the holomorphic discrete series contribution does.Moreover, we obtain an explicit formula for the formal dimensions of the holomorphic discrete series embeddings, and we interpret the holomorphic discrete series contribution to L2(G/N,ψ) as boundary values of holomorphic functions on a domain Ξ in a complexification GC of G forming a Hardy type space H2(Ξ,ψ).