Protection of local agriculture from invasive pest insects is critical for adequate and sustainable crop production. Important to this objective is the ability to accurately distinguish foreign from closely related domestic species, a process that has traditionally required identification using diagnostic morphological keys that can be both subtle and labour-intensive. This is the case for the mealybugs that include several important agricultural pests with cryptic morphological characters.ADNAbarcoding methodology was used to identify a destructive mealybug species recently reported from cotton and vegetables in different regions of Swaziland. A fragment of the mitochondrial cytochrome oxidase subunit I (COI) gene was sequenced for specimens of mealybug collected from wild and cultivated host plants in Highveld, Lowveld and Lubombo regions. The sequences obtained were aligned and comparisons were made within the group and with GenBank sequences of morphologically identified species collected from Turkey, Japan and Israel. Mealybug specimens from five crops and seven wild host plants belonging to six families in the Highveld, Lowveld and Lubambo regions of Swaziland were identified to be the cotton mealybug, Phenacoccus solenopsis Tinsley (Hemiptera: Pseudococcidae). This is the first record of the invasive mealybug in southern Africa. The study has validated the efficacy of sequence diversity in the COI gene for identifying mealybugs. The risks this pest poses to crop production in Swaziland and neighbouring countries are discussed.