Abstract: The genomic DNA was isolated from leaves of Paulownia plants through the CTAB method without liquid nitrogen. The internal transcribed spacer (ITS) of rRNA and two intergenic spacers of psbA-trnH and trnF-trnF were amplified from the genomic DNA by PCR and then sequenced. Sequence analysis of the three DNA markers were conducted with software Clustal X7.0,and their phylogenetic trees were constructed with software MEGA3.1. The results showed three fragments of ITS,psbA-trnH and trnL-trnF was 600 bp,540 bp and 900 bp in length,respectively. Similarity of ITS sequence between the previously reported Paulownia tomentosa and Paulownia No.1 or No.2 was higher than 95%,but that between the P. tomentosa and No.3,No.4 or No.5 of Paulownia was less than 79%.Similarity of the trnL-trnF between the P. tomentosa and No.1 or No.2 of Paulownia both was 99.5%,and that between the P. tomentosa and No.3,No.4 or No. 5 of Paulownia was less than 70%.The results indicated that sequence of the psbA-trnH of Paulownia species in different cultivation places was very conservative and it could not provide enough information for the relationship of the species among Paulownia.Molecular identification demonstrated that Paulownia No.1 and No.2 represented P. tomentosa,and Paulownia No.3,No.4 and No.5 represented P. fortunei.

Key words: Paulownia, ITS, psbA-trnH, trnL-trnF, molecular identification