In order to provide high speed broadband access to users in next generation networks, Gigabit Ethernet-Passive Optical Network (GE-PON) has emerged as one of the most promising technologies. The evolution of the GE-PON technology permits the users to connect to the Internet via gigabit access networks, which contribute to the increase of the network traffic in not only downstream but also along the upstream direction. However, the increase of the upstream traffic may lead to network congestion and complicate the bandwidth allocation issue, thereby affecting the Quality-of-Service (QoS) requirements of the users. In this paper, we point out the performance degradation issue of Transmission Control Protocol (TCP) communications due to the unanticipated effect of Dynamic Bandwidth Allocation (DBA) mechanism employed in GE-PONs. When network congestion occurs, DBA fails to achieve efficient and fair sharing of the bottleneck bandwidth amongst a number of competing TCP connections. In order to overcome this shortcoming of the conventional DBA scheme, we envision an appropriate solution by controlling the TCP flows’ rates based upon packet marking. The envisioned solution, dubbed as PPM-TRC, aims at controlling the TCP throughput for achieving both high efficiency and fair utilization of the passive optical line. The effectiveness of the PPM-TRC approach, verified through extensive computer simulations, demonstrates its applicability in dealing with a large number of competing traffic flows.