Abstract: In this paper, we established and optimized the AFLP molecular marker technology of Salix spp. based on capillary electrophoresis as well as simplify analysis flow of AFLP in order to construct Salix spp.linkage mapping and the implement of molecular breeding.First,the highquality genomic DNA was extracted for AFLP analysis.Then the genomic DNA was completely digested by restriction enzyme and ligased with oligonucleotide adapters successfully. We got the products via preamplification and selective amplification. At last, the selective amplification products were analyzed by capillary electrophoresis. Results showed that improved CTAB method was selected to extract genomic DNA, 450 ng of genomic DNA was used in digestion with EcoRⅠ and MseⅠ for 2 hours respectively, and ligased overnight. In selective amplification, 0.3 mmol/L dNTP, 1.5 mmol/L Mg 2+ , 0.125 μmol/L primers, 0.025 U/μL polymerase and 20 times dilution of preamplification products were desirable. Through many repeats, this system has been proved to be feasible in Salix spp. AFLPcapillary electrophoresis analysis.