Using the endogenous homologous recombination of living organisms for cloning (HR-cloning) was first described in yeast and eventually in bacteria. Although not so widespread, this method allows the straightforward engineering of fusion proteins with the ability of exchanging elements from 1 nt to several kb within a plasmid. Therefore it can be used to manipulate codons or transcription factor target sequences as well as to study regulatory regions like full promoters or UTRs. Likewise, reporter markers can be exchanged having either N- or C-terminal variants. It also offers the possibility of engineering customized plasmids providing a different strategy to overcome difficulties in the cloning and editing of challenging DNA fragments. The manipulation steps are minimized and any recA1 bacteria strain is suitable for it. This method has been tested with common and customized plasmids with a range up to 15 kb. Its simplicity allows the implementation in any molecular biology laboratory without the requirement of any commercial Kit. I will discuss examples of HR-cloning on a wide variety of organisms, from plants to Drosophila.