Objective: To establish and optimize ISSR-PCR reaction system for Taraxacum mongolicum.Method: Based on the analysis of orthogonal design test

an orthogonal design was used to optimize the ISSR-PCR amplification system on T.mongolicum by three factors（Taq polymerase Mix

DNA template and primer） at two concentration levels

respectively.PCR program was optimized by single factor experiments.Result: The suitable PCR reaction system contained 15 μL Taq polymerase MIX（1.25 U Taq DNA polymerase

1.8 mmol·L-1 Mg2+

dNTPs 0.24 mmol·L-1）

0.3 μmol·L-1 primer and 5 ng template DNA in total 25 μL reaction solution.On this basis

16 primers were screened with stable amplification and rich polymorphism from 50 ISSR primers.The optimal annealing temperature for ISSR-PCR reaction was proposed by gradient PCR.Conclusion: It is a way to establisd the ISSR-PCR system for orthogonal design combining with single factor test.This optimized ISSR reaction system would provide the basis for the genetic analysis of T.mongolicum.