Objective To establish a new congenic inbred mouse strain carrying and expressing EGFP and Foxn1^nugene for cancer research including human glioma as well. Methods According to criterion of GB14923-2010, the male Foxn1^nu nude mice backcross the female C57BL/6-Tg (CAG-EGFP) transgenic mice for 10 times, Then identify the phenotype using the methods and equipment as below: fluorescent flashlight and matching glasses; multifunction vivo imager; fluorescence microscopy. Results The congenic inbred mouse strain named Foxn1^nu. B6-CAG-EGFP/SU (Soochow University). All the 14 biochemical loci are homozygous and same with Balb/c mouse in addition to the Pep3 loci ("b" type instead of "a" type). Peripheral blood lymphocyte count shows the lymphocytes occupy 15% of nucleated cells; T lymphocytes occupy 0.3%, meet the requirement of inbred strain of EGFP nude mice. Conclusions Established a new congenic inbred strain -Foxn1^nu.B6-CAG-EGFP/SU which both express EGFP stably, and own immunodeficiency with lack of T lymphocytes. The phenotype "b" of biochemical loci "Pep3" is the unique characteristic that distinguish SU to Foxn1^nu.