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This paper addresses the navigation problem of coordinating a team of heterogenous vehicles including an autonomous surface vehicle (ASV) and several autonomous underwater vehicles (AUVs). Specially, a dedicated acoustic navigation scheme has been proposed in it. Utilizing the underwater DGPS concept, together with a set of intelligent surface sonobuoys, the precise position of the concerned AUV carrying an acoustic pinger, could be estimated by the measured time of arrival(TOA) of acoustic signals and the DGPS positions of sonobuoys, which were collected and computed by the central control ASV via radio link. Thus the ASV can generate and allocate the waypoints to the AUVs, and also move above the central of mass of the AUVs. As a result, the team constituted with heterogenous vehicles could implement a coordinated search or rescue scenario as a whole. Compared with INS/GPS navigation system, AUVs adopting such novel method, need not come to the surface to calibrate their positions periodically, which may seriously disturb the team coordination and existed formation. While compared with classical acoustic navigation systems (LBL, SBL, etc.), higher precise positions of AUVs are conveniently achieved. Furthermore, the paper demonstrates the simultaneous LS navigation algorithm for the coordinated control scheme in detail. The challenge is on the novel method in this paper that but also allows us to easily handle with heterogeneity in coordinated control task for underwater activities.