Previous studies have shown that Tetrahymena citrate synthase and the Tetrahymena 14-nm filament protein are encoded by a single gene and translated from one species of mRNA, and that they are identical in terms of molecular weight, antigenicity, and some enzymatic properties. In this study, using two-dimensional gel electrophoresis, we demonstrated that the citrate synthase comprised pI 7.7 and 8.0 isoforms, while the 14-nm filament protein comprised three isoforms with isoelectric points of 7.7, 8.0, and 8.4. The amino acid sequences of the NH2-terminal portions of all isoforms were identical and the peptide maps with V8 protease were almost the same. In addition, when the citrate synthase activity of each isoform was measured after separation by non-urea isoelectric focusing without denaturing treatment, the pI 7.7 and/or pI 8.0 isoforms exhibited the citrate synthase activity, but the pI 8.4 isoform only found for the 14-nm filament protein did not possess this activity. These results suggest that the polymorphism of these isoforms is caused by some posttranslational modifications, and that it may have resulted in the different compartmentalization and functions of Tetrahymena citrate synthase and the 14-nm filament protein.