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Complex systems such as ships are composed of multiple heterogeneous subsystems and equipments interconnected to accomplish various missions. In civilian and defense naval domains, ships are usually operated as a fleet leading to mission readiness and maintenance management issues. PHM (Prognostics and Health Management) plays a key role for controlling the performance level of such systems, at least on the basis of adapted PHM strategies and system developments. Thus, engineering methods are required for developing such fleet-wide PHM systems enable to address monitoring, diagnosis and prognostics for health management of the underlying heterogeneous equipments/components defining the fleet. In relation to this context, the paper highlights some lessons learned from PHM engineering and applications focusing on monitoring, fault detection and mission prognostics in marine domain. Since challenges, involved with developing and implementing proactive fleet-wide management through PHM system, remain several, in a second part, the paper underlines some new issues with regards to PHM's processes previously addressed.