An optimal ISSR reaction system for Taiwania cryptomerioides was established with 25.0 μL reaction mixture made up of 40 ng genomic DNA,0.4 μmol/L primer,1.8 mmol/ L Mg2+,1.0 U Taq,0.2 mmol/L dNTP,and 2.5 μL 10×buffer.The PCR were performed as follows:4 min at 94℃,40 cycles of 45 s at 94℃,45 s at 51℃ to 56℃,and 2 min at 72℃,with a final extension of 7 min at 72℃.Ten polymorphic primers were screened using this reaction system.Twenty DNA samples from the wild population of T.cryptomerioides distributed in Lichuan City of Hubei Province were amplified by the 10 selected primers.The percentage of polymorphic bands was 61.97 %,Nei’s gene diversity and Shannon’s information measure were 0.136 9 and 0.216 0,respectively.