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Abstract The budding yeastSaccharomyces cerevisiaeis an excellent model organism for studying a variety of critical cellular processes. Traditional methods to knock in or ‐out at specific yeast loci utilize polymerase chain reaction‐based techniques, in which marker cassettes with gene‐specific homologies are integrated into the genome via homologous recombination. While simple and cost‐effective, these methods are limited by marker availability when multiple edits are desired. More recently, CRISPR‐Cas9 technology has introduced methods to edit the yeast genome without the need for selectable markers. Although efficient, this method is hindered by additional reagents and lengthy protocols to design and test unique guide RNAs and donor templates for each desired edit. In this study, we have combined these two approaches and have developed a highly efficient economical method to edit the yeast genome marker‐free. We have designed two universal donor templates that efficiently repair commonly used selectable markers when targeted by a novel guideRNA‐Cas9 designed to promoter regions inAshbya gossypiifound in most integration modules. Furthermore, we find our newly designed guideRNA‐Cas9 successfully multiplexes when multiple markers are present. Using these new tools, we have significantly improved the cost and efficiency to generate single or multiple marker‐free genetic modifications. In this study, we demonstrate the effectiveness of these new tools by marker‐free ablatingPRC1,PEP4, andPRB1vacuolar proteases typically inactivated before many biochemical and membrane‐trafficking studies using budding yeast.