Non-Abelian BPS vortices in SO(N) x U(1) and USp(2N) x U(1) gauge theories are constructed in maximally color-flavor locked vacua. We study in detail their moduli and transformation properties under the exact symmetry of the system. Our results generalize non-trivially those found earlier in supersymmetric U(N) gauge theories. The structure of the moduli spaces turns out in fact to be considerably richer here than what was found in the U(N) theories. We find that vortices are generally of the semi-local type, with power-like tails of profile functions.