Mealybugs are common insect pests that can cause significant damage to oil palms, including reduced yield and overall plant health. The mealybugs feed on the plant sap, which later excretes honeydew, leading to the growth of sooty mold, and impedes photosynthesis. The traditional morphological identification methods for mealybugs are very time-consuming and challenging, due to their diminutive size and similar characteristics between their developmental stages. In this research, we investigated the effectiveness of the Ef-1α and 28S rRNA genes for molecular identification of a mealybug species infesting oil palm plantations in Tawau, Sabah. The DNA was extracted from the mealybug samples and amplified with M51.9/rcM53-2, D2F/D2R, and D10F/D10R primers. The amplified regions of the identified Nipaecoccus nipae Tawau-isolate were sequenced and deposited in GenBank. Our results demonstrate the potential of molecular methods for quick and efficient identification of mealybug species, which can aid in developing appropriate control strategies.