one embodiment of the present invention provides a system that accommodates different clock frequencies in an ethernet passive optical network . the system receives a signal from an optical line terminal at an optical network unit and derives an olt clock . the system also maintains a local clock . the system further receives from the olt an assignment for an upstream transmission window , during which the onu can transmit an upstream data burst to the olt based on the local clock . the system adjusts the number of bits of the data burst without affecting the payload data carried in the data burst , thereby allowing the data burst to fit properly within the upstream transmission window and compensating for frequency differences between the local clock and the olt clock . the system transmits the data burst based on the local clock in the upstream transmission window .