The authors report the use of the CRISPR-Cas system in *Saccharomyces cerevisiae* for genome engineering. They demonstrate that the CRISPR-Cas components, including the Cas9 gene and a designer guide RNA (gRNA), exhibit robust and specific RNA-guided endonuclease activity at targeted endogenous genomic loci in yeast. By using constitutive Cas9 expression and a transient gRNA cassette, they show that targeted double-strand breaks can significantly increase homologous recombination rates of single- and double-stranded oligonucleotide donors. Additionally, co-transformation of a gRNA plasmid and a donor DNA in cells expressing Cas9 results in near 100% donor DNA recombination frequency. The study provides a foundation for a simple and powerful genome engineering tool for site-specific mutagenesis and allelic replacement in yeast.The authors report the use of the CRISPR-Cas system in *Saccharomyces cerevisiae* for genome engineering. They demonstrate that the CRISPR-Cas components, including the Cas9 gene and a designer guide RNA (gRNA), exhibit robust and specific RNA-guided endonuclease activity at targeted endogenous genomic loci in yeast. By using constitutive Cas9 expression and a transient gRNA cassette, they show that targeted double-strand breaks can significantly increase homologous recombination rates of single- and double-stranded oligonucleotide donors. Additionally, co-transformation of a gRNA plasmid and a donor DNA in cells expressing Cas9 results in near 100% donor DNA recombination frequency. The study provides a foundation for a simple and powerful genome engineering tool for site-specific mutagenesis and allelic replacement in yeast.