A method and apparatus for a multiple lane transmission system that provides both a low latency mode of operation, while at the same time, provides reduced lane-lane skew. The overall transmission system operates as a mesochronous system, whereby each clock domain of the transmission system is synchronized to the leaf nodes of a global clock tree. A phase aligner is then used to align the phase of both the bit and byte clocks of each transmission lane to the clock signal generated at the leaf nodes of the global clock tree.