A method for site-directed mutagenesis which generates highly efficient plasmids and which uses only two PCR primers. The primers incorporate the same site for a restriction nuclease, the recognition site of which is 5' to the cut; the linear PCR product treated with such a nuclease, therefore, does not contain the recognition site, but leaves overhangs which facilitate re-cyclization. The interior of the plasmid contains the desired mutation sequence, and the sequence of the overhang may be designed to be the native sequence.