In this article, we propose a two-layer-structure called hierarchical basis reachability graph that is useful for marking estimation in Petri nets that contain unobservable transitions. On the basis of a hierarchical partition of the set of observable transitions, a hierarchical basis reachability graph consists of a primary and a secondary structures. Simulation shows that the time-consumption to compute a hierarchical basis reachability graph is in general much less than that of computing the corresponding basis reachability graph. A marking estimation algorithm is proposed by the structural analysis of the corresponding hierarchical basis reachability graph.