It is intended to provide a breeding method whereby a lipid-producing fungus belonging to the genus Mortierella can be effectively and efficiently bred without resort to antibiotics. Transformation is carried out with the use of an auxotroph (for example, uracil auxotroph) of a fungus belonging to the Mortierella as a host. More specically speaking, a gene compensating for the auxotrophy, which is employed as a marker, is transferred into the host (the gene transfer step). Next, a transformant is selected by using the recovery from the auxotrophy as the marker (the selection step). The lipid-producing fungus may be M. aplina, for example.