Previous studies demonstrated highly inefficient gene editing in C. reinhardtii using conventional Cas9 and sgRNA genes (only 1 editing event using > 1.5 × 109 initial cells). Design and testing of a hybrid gene-within-a-gene construct (composed of a Cas9 gene containing an artificial intron with an inserted sgRNA gene) demonstrated that such constructs were functional both in tobacco cells and C. reinhardtii cells. In tests with C. reinhardtii, approximately one in every ~ 3 × 107initial cells contained an edited version of the targeted FKB12 gene (i.e., an average of ~ 3 colonies with an edited FKB12 gene per electroporation using 108 initial cells). Lack of an intact Cas9/intron-sgRNA gene in cells carrying either of two different edited genes strongly suggested that editing was due to transient expression of the Cas9/intron-sgRNA gene and the likely toxicity of long-term expression of Cas9 in C. reinhardtii cells. Co-transformation of the arginine-requiring mutant, arg7-8, with Cas9/intron-sgRNA constructs and appropriately designed synthetic, 80 nucleotidessDNAs complementary to the argininosuccinate lyase (ARG) gene led to successful homologous recombination or nucleotide replacement and production of arginineprototrophs. As a practical application, a similar ssDNA oligonucleotide targeting the acetolactate synthase (ALS) gene and an appropriate Cas9/intron-sgRNA construct was used to create cells resistant to the herbicide, sulfometuron methyl.