The electrodialysis (ED) method has been employed successfully to remove organic salts from fermentation broth. The efficiency of ED is strongly affected by the transport properties of ions and solutes through ion-exchange membranes (IEMs), that is, the conductivity of the IEM and the diffusion coefficient of neutral solutes through the IEM. Therefore, it is very important to select IEMs being suitable for ED desalination of fermentation broth based on the transport properties of IEMs. The conductivities of eight kinds of commercial IEMs and the diffusion coefficients of neutral solutes through the IEMs were measured, and ED experiments for the desalination of simulated 1,3-propanediol fermentation broth were carried out by using a combination of the eight IEMs. By comparing the efficiency of the ED process, the optimum IEMs were determined and the influences of transport properties of IEMs were discussed.