Genetic differences of Pelteobagrus fulvidraco populations from Zhujiang River were compared by morphological and molecular biological methods. The scatter diagram of principal component analysis revealed that the populations from Duliujiang River and Lijiang River pooled into one group

while those from Dongjiang River separated from Duliujiang River and Lijiang River. It indicated that Dongjiang River population had a certain morphological differentiations compared to other two populations，while there were few morphological differentiation between Duliujiang River and Lijiang River.The mtDNA D-loop sequence analysis of three populations showed that 176 variable sites and 36 haploid types were detected

there were similar base compositions among three populations

the content of A + T (59.6%) was higher than the content of G + C (40.4%)

the average gene flow was 3.234

there was a large gene exchange between three populations.The NJ tree of haploid type shows that the populations Lijiang River and Duliujiang River formed the first cluster which together with the populations from Dongjiang River formed the second cluster. The analyzed result of 21 microsatellite loci in three populations showed that 15 loci were high polymorphic(PIC>0.5)，the clustering result of three populations was in accordance with the result of mtDNA D-loop marker

all clustering results had a certain correlation with their geographical distribution. From the result of morphological and molecular analysis，a conclusion can be drawn that the morphology in three populations had certain difference，there was rich genetic diversity among populations.