Problem of graph bi-partition (related to graph isomorphism)
Your problem is NP-complete. Two-colorable perfect matching (which is NP-complete even when restricted to cubic planar graphs) is reducible to your problem. Take $H_1$ and $H_2$ to be perfect matchings each of $|V|/2$ nodes. Then your problem is to find 2-coloring of $V$ such that each color class induces a perfect matching.