Levels of endogenous amino acid pools were measured for two species of the unicellular green alga Chlamydomonas. In C. reinhardtii, opposite mating types, designated + and −, of strain 137c were examined. The soluble pool of glutamic acid was most abundant in strain 137c−. In strain 137c+ similar levels of this amino acid were present, and high levels of cystine were observed. A soluble pool for the amino acid methionine was not detected in either strain. In opposite mating types of C. eugametos (strain Nos. 9 and 10), a soluble pool of alanine was most abundant, whereas neither cystine nor methionine were detected. When C. reinhardtii strain 137c+ was grown in the dark, cystine was not detectable, and proline markedly increased. Similarly, growth of strain 137c+ on nitrogen-deficient medium supplemented with a limited amount of arginine as a nitrogen source resulted in an apparent disappearance of pools of cystine. No apparent difference in the growth patterns of strains 137c+ and 137c− was observed. Tetrad analysis indicates that the high cystine content found in strain 137c+ is neither a characteristic of mating type nor under control of a single Mendelian gene. Key words: Chlamydomonas reinhardtii, Chlamydomonas eugametos, amino acid pool, cystine.