Saccharomyces cerevisiae produces two chitin synthases (Chs1 and Chs2) encoded by separate genes. Although these enzymes catalyze the same reaction, Chs2 is essential for septum formation whereas Chs1 has a repair function. To determine if these physiological differences are reflected in the enzyme structures, the CHS2 gene was sequenced and compared to that of CHS1. The predicted amino acid sequence of Chs2 shares substantial similarity with that of Chs1 in the carboxyl two-thirds of the protein. The amino one-third segments differ in predicted isoelectric point by almost 5 pH units. It is suggested that the similar regions are related to common catalytic function. The unrelated regions may be involved in regulation or localization of the respective enzymes. CHS1 and CHS2 are unlinked but may have arisen from the duplication of an ancestral gene.