In the early 90s the Asian tiger mosquito Aedes albopictus reached Europe, rapidly expanding in all the continent then becoming the main vector for human arboviruses. For some years, two additional invasive Aedes mosquito species, Aedes japonicus and Ae. koreicus, are circulating in several European countries posing potential health risks to humans and animals. Vector control is the main option to prevent mosquito-borne diseases, and an accurate sequence of the genome of these mosquitoes is essential to better understand their biology and to develop effective control strategies.We use short and long-read sequence data to perfom de novo assembly, polishing and purged haplotigs. Thus, we obtained Akor1 and Ajap1, assembly of the genomes of Aedes koreicus and Ae. japonicus. Their quality was ascertained using various metrics. Masking of repetitive elements, gene prediction and functional annotation was performed. Sequence analysis revealed a very high presence of repetitive DNA and, among others, thermal adaptation genes and insecticide-resistance genes. The assembly of the Akor1 and Ajap1 genomes constitutes the first updated collective knowledge of the genomes of both mosquito species, providing the possibility of understanding key mechanisms of their biology such as the ability to adapt to harsh climates and to develop insecticide-resistance mechanisms. Moreover, the microbiota of different populations of Ae. koreicus and Ae. japonicus was analysed by metagenomics. These studies have highlighted some population-specific symbionts and identified bacteria plausibly involved in the mechanisms of thermal-adaptation and insceticide-resistance. Collectively these results may help develop control methods to counteract the dispersal of these vectors.