It is well known that FAW in its native range consists of two strains, the so-called C-strain and R-strain, which are usually distinguished by mitochondrial markers and SNPs in the Z-linked TPI gene. Both genomes have been sequenced and annotated, and differ by as much as 2%. In previous Quantitative Trait Locus (QTL) analyses, we identified genomic loci that significantly affect phenotypic differences between the two strains, such as timing of mating at night, sex pheromone variation and hybrid behavioral sterility. Whether both strains have invaded the rest of the world is a question that arises in most publications on invasive FAW populations. Most analyses show that both mitotypes and only the C-type of TPI are found, which has led to the conclusion that the C-strain and RC-hybrids, but not the R-strain have invaded the rest of the world. However, genome-wide analyses show large variation in the nuclear genome, indicating not only multiple introductions in all invaded areas, but also that both strains have most likely invaded, resulting in genomes that are mosaics of C and R. To understand the genetic basis of variation in sex pheromone signal and response, host plant range, and differential responses to biocontrol agents, such as viruses, it is important to map all genomic SNPs and/or reads of phenotyped individuals onto the two separate native genomes. Such Genome-Wide Association Studies (GWAS) can identify genomic loci that underlie behavioral differences. Markers in these loci can be used to develop population- and region-specific management strategies.