It is of theoretical and practical significance to understand the mechanism of enzyme adaptation to acidic and alkaline environments and classification of them based on sequence information. In present work, the amino acid composition of 105 acidic and 111 alkaline enzyme sequences was systematically analyzed. Acidic enzymes contained significantly more Trp, Tyr, Thr and Ser, whereas less Glu, Lys, Met and Arg. On the other hand, alkaline enzymes have slightly more Trp, Ala and Cys, whereas less Lys, Arg and Glu. The amount of Ala, Glu, Leu, Asn, Arg, Ser and Thr in acidic and alkaline enzymes varied largely. Hence, a weighted amino acid composition method was developed for the discrimination of acidic and alkaline enzymes. Using the back-check and the 5-fold cross validation methods, the overall accuracy could reach 86.1% and 83.3%, respectively. A new method to classify acidic and alkaline enzymes based on their sequences was established.