This paper addresses the bipartite output consensus problem of heterogeneous multi-agent systems, where the agents have different dynamics. Under the assumption that the communication topology has a spanning tree and the information of the leader is accessible only to a fraction of followers, an adaptive distributed bipartite observer is designed for every follower to estimate some information of the leader. By combining the output regulator equation and reduced-order observer design, an output feedback control law is proposed for solving the bipartite output consensus problem. At last, a simulation example is provided to show the effectiveness of the theoretical results.