Objective: To establish the optimum ISSR-PCR system of Polygonum capitatum. Method: The Mg2+

dNTPs

primers and Taq DNA polymerase

were investigated to optimize the ISSR-PCR reaction system of Polygonum capitatum by orthogonal tests. Result: The optimized ISSR-PCR system of P.capitatum included 1×DNA polymerase buffer (10 mmol ·L-1 KCl

8 mmol ·L-1 (NH4)2SO4

10 mmol ·L-1 Tris ·HC1

pH 8.0)

3.0 mmol ·L-1 MgCl2 200 μmol ·L-1 dNTPs

2.0 U ·25 μL-1 Taq DNA polymerase

0.25 mmol ·L-1 primer

40 ng ·L-1 DNA template

in 25 μL PCR reaction systerm. By temperature gradient PCR

the optimum annealing temperature was determined as 48 ℃. Conclusion: The optimized system laid the groundwork for ISSR molecular analysis of P.capitatum Buch-Ham.ex D.Don.