In this study we analyzed the genetic diversity and phylogenetic relationships of six populations of cultured Litopenaeus vannamei (S1, S2, G1, K1, G2, and Sg) by sequencing their partial DNA sequence of the mitochondrial (mtDNA) control region. The results showed that 144 out of 146 haplotypes were unique for different populations, and the other 2 haplotypes were shared by S1 and S2. The haplotype diversity (Hd) was 0.42−0.99 in the 6 populations, and the nucleotide diversity (π) was 0−0.08. The population with the highest haplotype diversity was K1 (Hd=0.99±0.01), and the population with the highest nucleotide diversity was S2 (π=0.08±0.04). S1 had the lowest genetic diversity (Hd= 0.42±0.08, π=0.00), while S2 showed the highest genetic diversity (Hd=0.88±0.02, π=0.08±0.04). The AMOVE analysis suggested that the genetic difference between different populations (46.98%) was slightly lower than that within the population (53.02%). Fst values of genetic differentiation between populations were all positive (0.173−0.974), which indicated remarkable genetic differentiation between the 6 populations. The UPGMA phylogenetic tree (based on the genetic distance) and the NJ dendrogram (based on haplotype clustering) showed that the evolutionary tree was divided into two branches: S1 and S2 belonged to one branch. G1, G2 and Sg clustered first, and then converged with K1 to form another branch. For the 6 populations the clustering relationship based on haplotype was similar to that based on the genetic distance. The genetic differences between males and females within a population was minimum, but the degrees of inter-population genetic differences varied slightly or significantly. We compared the genetic parameters of individuals with different growth rates in the same population and found that there might be a certain degree of genetic differentiation between the fast-growing and slow-growing groups. We also analyzed the genetic differentiation between populations purchased at different time from the same company. It showed that the Fst value between populations purchased with longer interval (7 to 9 months) from the same company might be greater than that between populations purchased from different companies.