Almost all research on Chlamydomonas reinhardtii has utilized wild-type strains of three principal stock lines (Sager, Cambridge, Ebersold-Levine), which traditionally has been assumed to be descendants of a single zygote isolated by Smith. We previously noticed that there are several sequence differences in a single-copy gene of gametolysin, mmp1, between the mt+ and mt- strains employed. To further examine the polymorphisms among the three lines, we obtained 18 representative strains of all three descendant lines of Smith's isolate, nine strains recently isolated from the wild and one strain (CC-1373 mt+) of C. smithii, a strain from Smith's collection interfertile with these C. reinhardtii strains; and we compared the mmp1-3'UTR by RFLP and sequencing analyses. Sequence divergences were found between the mt+ and mt- strains of both the Sager and Cambridge lines, but not between the two mating-type strains of the Ebersold-Levine line. We also examined the polymorphisms, using the 3'UTRs of two other mmp genes and the introns of ypt4 and fus1. Based on the results, we conclude that it is genetically impossible for all the current C. reinhardtii lines to be the immediate descendants of a single zygote.