Population genetic structure and genetic diversity of three populations of Coilia ectenes sampled from Yangtze River from 2002 to 2003 were revealed by RAPD-PCR and ISSR-PCR markers.There were 110 bands occurring in the three populations assayed by RAPD-PCR with fifteen 10-base primers,and the polymorphism was from 0.490 to 0.657,Shannon diversity index was from 18.63 to 22.38,and mean Nei's genetic distance was from(0.1195) to 0.1454.In the meanwhile,there were 67 bands occurring in the three populations revealed by ISSR-PCR with 11 primers,and the polymorphism was from 0.576 to 0.682,Shannon diversity index was from 11.56 to(13.66),and mean Nei's genetic distance was from 0.1169 to 0.1467.These data respectively from the two markers were significantly positively correlated(r=0.95,P<0.05).AMOVA analysis showed that the genetic variation between sampling years of the three populations accounted for less than 1.1% of the total one,while this variation between populations sampled in one year accounted for 6.99% revealed by RAPD-PCR or 2.75% by ISSR-PCR of the total one.It also showed that the genetic variation among samples within a population was the principal component,which accounted for more than 96% of the total one at P<0.000 1 assayed by the both markers.AMOVA results suggested that there was no significantly genetic diversity among the three populations of(C.ectenes),and this was confirmed by Neighbor-joining dendrogram constructed based on matrices of pairwise(Nei's) genetic distances among samples.Although the pairwise Nei's genetic distances among samples and the Neighbor-joining dendrogram from RAPD-PCR was not positively correlated with those from ISSR-PCR according to the Mantel test and the cluster analysis respectively,ISSR-PCR could reveal higher polymorphism in the tested populations.