The development of molecular cloning techniques starting in the late 1960s created new tools to facilitate our understanding of gene function. Later advances in PCR and site-specific mutagenesis allowed researchers to efficiently dissect genes down to the single-nucleotide level. These methods have become virtually ubiquitous in nearly every biology laboratory. Recently, we developed an additional technique called SIMPLE (SapI/AarI incision-mediated plasmid editing), which allows for efficient deletions, short insertions (e.g., epitope tagging), and accurate mutations of episomal plasmids. SIMPLE cloning has a wide range of applications for molecular geneticists and adds a precision instrument to the biologist’s toolbox. Here, we describe a detailed, step-by-step set of instructions for SIMPLE cloning.