In this study, 21 species, varieties and forma in Paulownia were used to detect the genetic relationships by using inter-simple sequence repeats （ISSR） markers. The results showed that： 1 ） A total of 85 DNA fragments were amplified using 9 out of 100 ISSR primers with unambiguous unique polymorphic bands, among which 74 DNA bands were polymorphic （ PPB = 87.05 % ） , indicating significant genetic differentiation among Paulownia accessions tested ; 2） The dendrogram was constructed with MEGA3.1 statistical package using UPGMA （the unweighted pair-group method with arithmetic average）, with which Paulownia was roughly divided into three main groups of Paulownia tomentosa group, P. fortunei group and P. fargesii group. The Paulownia germplasms with close geographical distribution were clustered together, which illustrated there was a close relationship among them ; 3） The findings of the relationship and classification were basically consistent with the morphology, cytology, isozyme study results among P. elongata, P. lamprophylla, P. elongata f. alba, P. catalpifolia, P. henanensis, P. tomentosa var. lucida, P. tomentosa, P. fortunei, and P. fargesii. At the end of this paper, the taxonomy of some Paulownia species was discussed. Some specific bands of Paulownia species, detected in this research, could be furthermore converted into SCAR marker.