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WDM-PONs have recently emerged to provide dedicated and separated point-to-point wavelengths to individual optical network units. In addition, the recently standardized Ethernet OAM capabilities under the IEEE 802.1ag standard and ITU-T Recommendation Y.1731, together with state-of-the-art optical timedomain reflectometry provide new link-layer and physical tools for the effective troubleshooting of WDM-PONs. This article proposes an integrated troubleshooting box (ITB) for the effective combination of both physical and link-layer information into an effective and efficient set of management procedures for WDM-PONs. We show its applicability in a number of realistic troubleshooting scenarios, including failure situations involving either the feeder fiber, one of its branches, or even Ethernet links after the ONU.