Abstract:Thirty-eight provenances of Paulownia fortunei were used to detect the genetic diversity and genetic differentiation by inter-simple sequence repeats (ISSR) analysis. The results showed that: (1)A total 95 DNA fragments were amplified using 9 primers with unambiguous unique polymorphic bands screened from 100 ISSR primers, polymorphic loci of which were 88 (PPB=92.63%). (2)At the species level, the mean values of effective number of alleles (Ne) , Nei’s gene diversity index (H) and Shannon’s Information index (I) among provenances were 1.391 0, 0.242 4 and 0.376 5, respectively, the percentages of polymorphic loci (PPL) among different provenances were between 32.63% (Fuzhou, Jiangxi) and 56.84% (Wu Zhou, Guangxi and Jiu Jiang, Jiangxi) with an average of 47.16%; Gene flow among populations (Nm) was 0.912 7, the coefficient of population differentiation (Gst) was 0.353 9, which estimated that the genetic variation between provenances account for 35.39%, indicating that the genetic variation between provenances was higher than that of within provenances. (3)Genetic identity ranged from 0.39 to 0.82, reflecting the relatively wide genetic basis among P.fortunei provenances. Thirty-eight provenances of P.fortunei could be divided into 3 major groups obviously based on the UPGMA cluster analysis. A rotated PCoA plot with the markers as observations was constructed to determine 4 big groups. Principal coordinates analysis (PCoA) for ISSR data did not give the same result with the UPGMA cluster, the corresponding discussion was made in the paper. The test also illustrated that there was no significant correlation between genetic and geographic distances among provenances.