Objective: To optimize simple sequence repeat-polymerase chain reaction(SSR-PCR) system for providing a reference to genetic diversity and phylogenetic analysis among germplasms of Eucommiae Cortex. Method: Orthogonal design and single factor tests were adopted to optimize SSR-PCR system of Eucommiae Cortex with Taq DNA polymerase

template DNA

Mg2+

primers and dNTP concentration as factors

test data were analyzed by SPSS software. Result: Effects of each factors were in the order of Mg2+>Taq DNA polymerase>primers>dNTP>DNA template.Optimal reaction system was as follows:10×PCR buffer of 2 μL

Taq DNA polymerase of 0.5 U

Mg2+ of 1.25 mmol · L-1

dNTP concentration of 0.2 mmol · L-1

primers of 0.3 μmol · L-1 and DNA template of 60 ng in 20 μL reaction solution. Conclusion: Bands are bright and clear with good stability and reproducibility by amplification of this optimized SSR-PCR system

it is suitable for genetic diversity and phylogenetic analysis among germplasms of Eucommiae Cortex.