The codling moth (Cydia pomonella (L.)) is an invasive pest of pome fruits introduced to the Americas in the 19-20(th) centuries. This pest is widespread on both sides of the Andes range separating Argentina and Chile. We performed an analysis of the population genetic variability and structure of C. pomonella in Argentina and Chile using 13 microsatellite markers and sampled C. pomonella from apple as the main host plant along its distribution area (approx. 1,800 km). A total of 22 locations (11 from Chile and 11 from Argentina) were sampled. Significant genetic differentiation was observed among samples from Argentina and Chile (F-SC = 0.045) and between all localities (F-ST = 0.085). Significant isolation by distance (IBD) was found for each country and when samples from both sides of the Andes range were pooled, although a lower correlation coefficient was observed. The Mantel test showed that the geographic distance and highest altitude of the mountains between locations were significantly associated with the pairwise F-ST when samples from both sides of the Andes range were pooled. According to a Bayesian assignment test (STRUCTURE), samples from Argentina and Chile conformed to two distinct genetic clusters. Our results also suggest that the recent invasion of C. pomonella in the southernmost localities (Aysen Region in Chile and Santa Cruz Province in Argentina) originated in populations from the respective sides of the Andes range. Our results indicate a genetic exchange of C. pomonella within each country and significant genetic differentiation between countries, which could be explained by dispersal mediated by human activities related to fruit production within each country with little exchange between them. A possible explanation is that the Andes range could be a significant barrier for dispersal by flight, and quarantine barriers could prevent the movement of plant material or infested fruit between countries.