Classical rheological methods are often insufficient to characterize and to differentiate the non-linear rheological behavior of polysaccharide systems such as carrageenan or starch. In this article the non-linear rheological method of characteristic functions is used to discriminate between the different polysaccharides. This method is based on the Fourier transform-rheology (FT-rheology). The response of a sample is decomposed using simple characteristic functions. We show that there are differences in the response of a number of carrageenan and starch samples, which are not distinguishable with classical rheometry.