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In order to enable new services that require high data rates over longer distances, the optical fiber substitutes the copper cable step by step in the access network area. Time division multiplexed - Passive optical network (TDM-PON) is a fast emerging architecture that uses only passive components between the customer and the central office. PON operators need a monitoring system for the physical layer to guarantee high service quality. This monitoring system is necessary during the fiber installation, final network installation testing, regular operation of the network, and for fault localization. First, in this paper, we present the motivations, requirements and challenges of TDM-PON monitoring. Second, we make an exhaustive review of the monitoring techniques and systems for TDM-PON, mostly proposed within the last five years. In our survey we include the approaches already available in the market even with limited performance and those still in research. Third, we make a detailed classification of all these approaches and qualitatively compare characteristics in a list of performance parameters and aspects. Finally, we outline open issues and future research perspectives in physical layer PON monitoring that may target higher performance, lower cost, or scalability to next generation PON architectures. This includes wavelength division multiplexing (WDM), TDM over WDM or long-reach PONs intended to extend the reach from 20 up to 100 km distances and beyond.