The existence of genetic differences among Australian populations of the pest moth Helicoverpa armigera based on microsatellite markers is contentious. To resolve this issue, we analyzed microsatellite variation in moth samples from multiple locations simultaneously in two laboratories that have previously reported contrasting patterns. Alleles and allele numbers detected in the laboratories differed, as did the genetic differences found between the samples. The automated scoring system used in one of the laboratories combined with non-denaturing polyacrylamide gels led to inaccurate identification of alleles and high FST values between the populations. However, H. armigera in Australia is probably not structured geographically, with high gene flow between populations. This influences management of H. armigera and the development of area-wide control options, as populations need to be considered as one panmictic unit. The results also highlight potential problems of automated scoring systems when these are not checked carefully.