Morpholino oligonucleotide (MO) analogues derived from the homologous Ku70 gene were introduced via electroporation into protoplasts of Mucor circinelloides. Linear or circular vector DNA harbouring a functional leuA gene was added to transform the leucine auxotrophic Mucor circinelloides strain R7B to prototrophic growth. To distinguish homologous re-combination events from residual mutated leuA copy in hybridization analyses, the leuA gene in the vector was modified to carry a silent point mutation creating an additional XbaI restriction site. In all stable transformants, vector parts outside of the leuA gene are not co-integrated into the genome. One transformant shows a large duplication of the leuA genomic region. The MO approach adds a novel and versatile tool to the repertoire of genetic manipulation instruments in zygomycetes that are still only rudimentarily amenable to molecular analyses.