Random amplified polymorphic DNA method was used to investigate the genetic diversity of Anguilla japonica including five samplings collected from 4 locations,totally 92 individuals(10 premature adult eels,82 glass eels) in 2005 from the Yangtze River Estuary.51 RAPD primers were synthesized and 16 primers were selected and used.A total of 132 loci were amplified,of which 114 loci(86.36%) were polymorphic.Average heterozygosity(Hc) and genetic diversity index(Ho) of five samplings by Shannon index varied form 0.205 3 to 0.315 0,and 0.297 4 to 0.452 6 respectively.Fixation Index FST between two samplings varied from 0.050 8 to 0.152 4.Partition of total genetic variation indicated that 79.12% was contributed within populations and 20.82% among samplings.The Nei's genetic distances of five samplings varied form 0.059 3 to 0.142 5.There is no significant relationship between the genetic variation of samplings of glass eel and the sampling time or the sampling area.It indicates the all studied glass eels might be originated from one big complex population.But the results from genetic distance,Fixation Index FSt and NJ tree all showed,a rather high difference in genetic distance and genetic diversity could be exist between the premature adult eels and glass eels.