The internal transcribed spacer 1 (ITS-1) of four common carp populations were amplified and sequenced.The result showed that the average contents of GC were obviously higher than that of AT in the aligned sequences of 370bp.Total 34 variable sites were detected, and 14 haplotypes were recovered.The haplotype diversity and nucleotide diversity were 0.637±0.055 and 0.00857±0.00200, respectively.The genetic distance between Heilongjiang carp and Jian carp displayed the highest, up to 0.10129, while that between Heilongjiang carp and Yellow River carp peculations was the lowest to 0.02305.The fixation indices (F_st) of analysis of molecular variance (AMOVA) among populations was 0.05373, which showed no significant population structure.Tlie phylogenetic tree of ITS-1 built with MEGA 4.1 showed that four common carp populations were clustered into two major clades based on genetic distance.Populations of Heilongjiang carp and Yellow River carp were clustered in northern clade, while Jian carp and Hebao red carp were clustered in southern clade.