ABSTRACT The first two non-Mendelian gene mutations to be identified in Chlamydomonas moewusii are described. These putative chloroplast gene mutations include one for resistance to streptomycin (sr-nM1) and one for resistance to erythromycin (er-nM1). In one- and two-factor reciprocal crosses, usually over 90% of the germinating zygospores transmitted these mutations and their wild-type alternatives from both parents (biparental zygospores); the remaining zygospores transmitted exclusively the non-Mendelian markers of the mating-type "plus" parent. Among the biparental zygospores, a strong bias in the transmission of non-Mendelian alleles from the mating-type "plus" parent was indicated by an excess of meiotic and postmeiotic mitotic progeny that were homoplasmic for non-Mendelian alleles from this parent compared to those that were homoplasmic for the non-Mendelian alleles from the mating-type "minus" parent. At best, weak linkage was detected between the sr-nM1 and er-nM1 loci. Non-Mendelian, chloroplast gene markers in Chlamydomonas eugametos and Chlamydomonas reinhardtii showed a predominantly uniparental mode of transmission from the mating-type "plus" parent in crosses performed under the same conditions used for the C. moewusii crosses.