Method, system and network device for programming lane alignment markers are provided. The method includes configuring the first port having a plurality of sub-ports, as at least a dual lane port where each lane of the dual lane port is configured to receive and transmit frames; negotiating with the first network device to determine a lane alignment marker that is acceptable by the first network device; and programming the first port to identify the lane alignment marker associated with the vendor of the first network device for processing frames received from the first network device and transmitted to the first network device.