The purpose of this study was to develop a membrane filtration method to isolate uninuclei conidium of Aspergillus oryzae, then the method was adopted to develop a transformation system of A. oryzae. A. oryzae 3.951 contained 1–4 nuclei in each conidium. The percentages of uninucleate and binucleate conidia were approximately 16.15 and 74.22%, respectively. Conidia suspension was filtrated with a 5-μm membrane to overcome the bottleneck caused by multinucleate conidia and to remove excess multinucleate conidia before UV mutagenesis. Uninucleate conidia of 5-fluoroorotic acid (5-FOA)-resistant strains were enriched by filtration with a 3-μm membrane. The pyrG mutant strain AS11 was obtained and GFP-pyrG was successfully transformed into AS11.