Since it was observed that the structural class of a protein is related to its amino acid composition, various methods based on amino acid composition have been proposed to predict protein structural classes. Though those methods are effective to some degree, their predictive quality is confined because amino acid composition cannot sufficiently include the information of protein sequences. In this paper, a measure of information discrepancy is applied to the prediction of protein structural classes; different from the previous methods, this new approach is based on the comparisons of subsequence distributions; therefore, the effect of residue order on protein structure is taken into account. The predictive results of the new approach on the same data set are better than those of the previous methods. As to a data set of 1401 sequences with no more than 30% redundancy, the overall correctness rates of resubstitution test and Jackknife test are 99.4 and 75.02%, respectively, and to other data sets the similar results are also obtained. All tests demonstrate that the residue order along protein sequences plays an important role on recognition of protein structural classes, especially for a/b proteins and a'/b proteins. In addition, the tests also show that the new method is simple and efficient.