According to the Chile jack mackerel (Trachurus murphyi) samples in the southeast Pacific Ocean (34°S ~37°S,90°W-110°W) collected by Chinese trawler fishing vessel during July and December 2009, 146 muscle samples collected from17 sites were used for population genetic structure identification by Random Amplified Polymorphic DNA (RAPD) analysis. 52 loci were detected and 51 of these loci were polymorphic, which accounted for 98.08% of the total loci. The Shannon’s index was 0.5202±0.1813, the Nei’s genetic diversity index was 0.3500±0.1440, and the GSTvalues was 0.0311. The results indicated that the genetic diversity of the Trachurus murphyi was comparably high, and genetic differentiation was not significant among populations.