After six-generation selection successively, Fenneropenaeus chinensis showed better economical traits such as fast growth and disease-resistance and so on. The average body length and the weight of each selective population increased by 8.4% and 26.86%, respectively, compared to the control. The morbidity was less than 10%, while it was more than 40% in the control. Genetic structure of each generation was also analyzed in the paper, the results were as follows: (1) Isozyme analysis: thirteen loci were examined and five loci were polymorphic, i.e., MDH-2, GPI, MPI, PGM-2 and PGM-3. There were significant differences at the locus PGM-3, and the gene frequency showed a decreased trend. At MPI locus allele C was found at the cultured populations, and the frequency showed an increased trend. (2) RAPD analysis: RAPD technique was used to investigate the genetic structure of five generation successively. The proportions of polymorphic loci showed a decreased trend while there was no difference between fifth generation and sixth generation. The degree of genetic differentiation (G_(st)) was moderate between populations except third population and fourth population. (3) SSR analysis: eight loci were analyzed among five generations, and 108 alleles were detected. The average heterozygosities showed a decreased trend while sixth generation remained the level of fifth generation. The values of G_(st) were less than 0.05, which showed that there was differentiation to some degree but it was weaker.