The variety of the raw fruit is important for the quality of fruit juice. To punish the selling of fake apple juice and protect the legal rights of the consumers, it is necessary to discriminate the variety of apple juice. In this work, totally, 89 fluorescent spectra of the apple juice samples, which were produced by two kinds of apples from Xi’an and Yunnan, were measured. Among these fluorescent spectra, 62 fluorescent spectra were used to build the model based on support vector machine and the model was cross validation with leave one out cross validation method. The accuracy of the cross validation was 100%. The rest 27 fluorescent spectra were used to validate the model and the accuracy was 96.3%. All these results demonstrated that fluorescent spectroscopy combined with support vector machine is feasible to discriminate the variety of the apple juice.