A modified SMB system composed of two pumps was developed for the separation of L-ribose and Larabinose from its binary mixture. In two-pump SMB operation, the flow rates required for separation in every column zones and product ports are identical to those in conventional SMB equipped with four pumps and are controlled by appropriate operation of valves during a cycle of switching time. The purity, yield and enrichment of sugars obtained by two-pump SMB separation were comparable to that of conventional SMB. The two-pump SMB system is therefore considered to be more economically efficient than conventional SMB by reducing the cost for SMB installation and pump operation.