Abstract: The present study conducted four different radiation dose of 50 cGy, 100 cGy, 1 000 cGy and 1 500 cGy in order to research the new kind breeding of Marsupenaeus japonicus. In our study, the 60Co-γ radiation was conducted on the condition of 3.4 cGy/sec with M. japonicus which was about to spawn. We applied the AFLP molecular technology to analyze the genetic similarities, genetic distances and genetic diversity of the 60Co-γ-radiated progeny in each group. The weight data of M. japonicus progeny in each group grown in earth ponds over 90 days were also counted to supply the proof for the radiation breeding programme of M. japonicus. All those experimental data were conducted with single factor analysis of variance to test the difference. The experiment results indicated that the genetic similarities was from 0.873 7 to 0.894 7 and the genetic diversity of 60Co-γ-radiated progeny was not significant different from the control group in populations (P>0.05). But we found some obvious distinctions in the genome type of single individual in 60Co-γ-radiated groups compared to others which did not exist in control group. Meanwhile, the growth in earth ponds was significant different in each group. Our research provided fundamental data and science proof for the radiation breeding programme of M. japonicus.