Abstract: Methods for recombining a polynucleotides of interest comprising the step of generating a recombinant polynucleotide by PCR amplification using as a template a pool of oligonucleotides having a chain terminating agent, e.g. ddNTP, at the 3′ end. Such oligonucleotides are preferably short, e.g. to provide for a higher degree of recombination. The PCR amplification is preferably carried out under conditions inducing mutagenesis in the amplified polynucleotide product. Recombined and mutagenized polynucleotides can be used to rapidly evolve cells and/or organisms to enhance or depress a phenotype of interest.