The Western conifer seed bug, Leptoglossus occidentalis, is native to North America and has already been considered a significant pest in several European countries since its first observation in Italy in 1999. In Spain and Portugal, it was recorded for the first time in 2003 and 2010, respectively, and its impact on Stone Pine (Pinus pinea) is of major concern. Before developing control measures for this insect pest, it is paramount to clarify its spatiotemporal dynamics of invasion. Therefore, in this study, we aimed to (a) characterise the genetic structure and diversity and (b) invasion pathways of L. occidentalis populations in the Iberian Peninsula. To do so, specimens of L. occidentalis were collected at fourteen sites widely distributed within the Iberian Peninsula. We used mtDNA sequences of Cytochrome b and eleven microsatellite markers to characterise the genetic diversity and the population structure in the Iberian Peninsula. Our genetic results combined with the observational dates strongly support a stratified expansion of L. occidentalis invasion in the Iberian Peninsula proceeding from multiple introductions, including at least one in Barcelona, one in Valencia, and one in the west coast or in the Southeastern region.