Anaerobic treatment of maize seedlings results in the selective expression of 10 major and 10 minor polypeptides designated as anaerobic polypeptides (ANPs) (Sachs, M. M., Freeling, M., and Okimoto, R. (1980) Cell 20, 761-767). Enzymatic functions have been ascribed to two of these polypeptides, alcohol dehydrogenases I and II. This report identifies a third anaerobic polypeptide, a maize glucose phosphate isomerase. Glucose phosphate isomerase specific activity increased 60% in 24 h of anaerobiosis and to more than twice its original level in 72 h. Antiserum to spinach cytoplasmic glucose phosphate isomerase 1) was monospecific against maize protein, 2) reduced glucose phosphate isomerase activity in maize extracts by 60%, and 3) recognized a single polypeptide selectively labeled with [35S]methionine during anaerobiosis. This polypeptide co-purified with the major glucose phosphate isomerase of maize. Maize glucose phosphate isomerase co-migrated on two-dimensional polyacrylamide gels with ANP55, the anaerobic polypeptide with a molecular weight of 55,000 on sodium dodecyl sulfate-polyacrylamide gels. Electrophoretically distinguishable alleles of Phi 1 (phosphohexoisomerase-1 gene located at maize chromosome 1L-140) predictably altered the electrophoretic behavior of ANP55, thus proving that Phi 1 encodes ANP55 and that ANP55 is a glucose phosphate isomerase.