Invasive species pose a serious threat to ecosystems and biodiversity, leading to considerable economic losses for countries. The papaya mealybug (Paracoccus marginatus), is a prominent invasive pest that affects over 200 plant species and has been recorded in more than 60 countries and regions.Here, the chromosome-level genome of P. marginatus was assembled using PacBio and Hi-C technologies. The resulting genome, with a total size of 213.81 Mb, was organized into four chromosomes. The contig and scaffold N50 values were 20.2 Mb and 48.01 Mb, respectively. The genome assembly attained a BUSCO completeness score of 95.5%, and CEGMA analysis showed that 99.56% of the genome was thoroughly annotated. It includes 13,367 predicted protein-coding genes, with 49.26% of the assembly identified as repetitive sequences. This high-quality genome serves as a valuable resource for a range of research fields, such as population genetics, evolutionary studies, invasive species management, and comparative genomics within Hemiptera and other insect groups.