The aim of this study was to isolate protoplasts from endophytic fungi and to carry out self-fusion of protoplasts for their enhancement of metal resistance. Self-fusant CBRF59T3 with resistance to 25 mM Cd(II) was constructed by self-fusion of inactivated protoplasts from Mucor sp. CBRF59. The inoculation of CBRF59 and CBRF59T3 improved significantly the availability of Cd(II) and Pb(II) in the soil. Compared with CBRF59, CBRF59T3 inoculation increased the content of water-soluble Cd(II) by 24%. The dry weight of rape inoculated with CBRF59 and CBRF59T3 was both higher than that of the uninoculation rape. Inoculation of CBRF59T3 further increased the dry weight of rape by 62% than CBRF59 in the higher Cd(II)-+Pb(II)-contaminated soil. Compared with CBRF59, CBRF59T3 inoculation increased the concentration of Cd(II) in rape shoots by 35-189% in Cd(II)- and Cd(II)-+Pb(II)-contaminated soils. The inoculation of CBRF59T3 also enhanced the translocation of Cd(II) from roots to shoots and increased the amount of extracted Cd(II) by rape. The results indicated that the mutants constructed by protoplast fusion is a feasible and efficient method to improve stress tolerance of uncharacterized fungi for phytoremediation of soils contaminated by heavy metals.