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Although an AAPN (Agile All-Photonic Networks) network can allocate bandwidth dynamically according to the request from the edge nodes, congestion control is still required to handle degradation of network performance when network resources are depleted. This paper investigates the use of XCP (eXplicit Control Protocol) to handle traffic congestion in AAPN. Unfortunately, XCP requires congestion information along the data path and a fixed link capacity in the network, both of which are absent in an AAPN network. We remedy this by a cross-layer design of the congestion control scheme by integrating the AAPN signaling protocol with a modified version of XCP. Our NS2 simulations demonstrate that our modified XCP (XCP-A) can perform well in AAPN networks.