We introduce the concepts of marked multi-colorings, marked chromatic polynomials, and marked (multivariate) independence series for hypergraphs. We show that the coefficients of the q-th power of the marked independence series of a hypergraph coincide with its marked chromatic polynomials in q, thereby generalizing a corresponding result for graphs established in Chaithra et al. 2025 (arXiv:2503.11230). These notions are then naturally extended to subspace arrangements. In particular, we prove that the number of marked multi q-colorings of a subspace arrangement is a polynomial in q. We also define the (marked) independence series for subspace arrangements and prove that the (-q)-th power of the independence series of a hyperplane arrangement has non-negative coefficients. We further conjecture that the (-q)-th power of the independence series of a hypergraph has non-negative coefficients if and only if all its edges have even cardinality.