Simple sequence repeats (SSR) have been found to be abundant and highly polymorphic in a number of eukaryotic genomes. The objective of this study was to determine the presence and variability of (CA/GT)n SSRs in the genome of the alga Chlamydomonas. A genomic DNA library of C. reinhardtii was screened with a radiolabeled (AC) 11 probe for the presence of (CA/GT)n repeats. The positive clones were sequenced. Three PCR primer sets flanking the (CA/GT)n sequences were constructed, and the Polymerase Chain Reaction (PCR) was used to specifically amplify these regions from several Chlamydomonas species and multiple isolates of C. reinhardtii. All three loci were highly polymorphic in the C. reinhardtii isolates. A simple Mendelian inheritance pattern was found for all three loci, which showed 2:2 segregation in the tetrads resulting from a cross between C. reinhardtii and C. smithii.