Purification of high added value products obtained by fermentation processes is a key research task in current biotechnology, especially the ones concerning proteins of very similar molecular structure such as isoenzymes. Purification and separation of biomolecules by commercial ion exchangers is an attractive alternative to affinity chromatography due to its availability and lower cost. For this reason and for its high uptake capacity there is an increasing interest in the application of ion exchangers in biotechnological downstream processing. In this paper, the kinetics of ion exchange of the two isoenzymes of glucoamylase from Aspergillus niger on the anion exchanger DEAE-Toyopearl 650 have been investigated in a batch stirred tank. The experimental results were fitted to a mathematical model accounting for both external fluid film mass transfer resistance and pore diffusivity. In addition, the kinetic parameters involved in the process have been obtained for each isoenzyme.