During amino acid sequence studies of carbonic anhydrase (CA) III, purified from a pool of human skeletal muscles, and electrophoretically undetectable (silent) variation was found at residue 31 which was either valine and/or isoleucine. To distinguish a simple allelic polymorphism from more complex models involving gene duplication, 11 separate CA III samples were purified from individuals of different age and racial backgrounds. Peptide mapping by high performance liquid chromatography and sequencing indicated that four were homozygous for 31-Val, three homozygous for 31-Ile and four were apparent heterozygotes. Since the ratio of Val/Ile at residue 31 was approximately 1.0 in the heterozygotes, the present observations are consistent with a simple allelic polymorphism model. Despite the small sample size, there are preliminary indications that the gene frequencies may differ among racial groups. The finding of this silent allelic polymorphism together with the finding of an electrophoretically detectable polymorphism of CA II permits us to test the linkage of the CA II and CA III genes which appear to have been formed by gene duplication more than 300 million years ago. The possibility that the Val/Ile variation may represent a neutral mutation is discussed.