Morphological and molecular studies of invasive insect pests are vital for their precise identification, monitoring, and management. These studies provide insights into their morphology, genetic diversity, and evolutionary adaptations, which are crucial for developing effective control measures. Two invasive whiteflies, Aleurodicus rugioperculatus Martin and Paraleyrodes bondari Peracchi, were found to be causing significant damage to coconut plantations in Tamil Nadu, leading to considerable losses for farmers. In light of this, a survey was conducted during 2020 and 2021 to assess the incidence of these two whitefly species (A. rugioperculatus and P. bondari) in coconut (Cocos nucifera L.) plantations across Tamil Nadu, India. Nymphs and adults were collected from coconut fields and morphologically identified through live photographs and slide-mounted specimens. Morphological identification revealed distinctive traits for each species. Pupae of A. rugioperculatus exhibited a rugose operculum with a triangular lingula, compound pores featuring a dagger-like process, and smaller compound pores on segments VII and VIII. Adults displayed irregular light brown bands on their wings, while smaller males had a long, pincer-like structure at the end of the abdomen. In contrast, P. bondari was distinguished by flower-petal-like ovoid facets on the puparium’s abdominal compound pores, and adults showed "X"-shaped oblique greyish stripes on their wings. Further molecular confirmation was achieved through polymerase chain reaction (PCR) amplification and sequencing of the mitochondrial Cytochrome Oxidase subunit I (COI) gene. A 650 bp fragment was successfully amplified, and the resulting sequences showed a 100% match with available sequences in GenBank, confirming the species identities of A. rugioperculatus and P. bondari. Phylogenetic analysis of the COI gene sequences, conducted using MEGA-11 software and the maximum likelihood method, produced a dendrogram clustering the specimens into a single clade with distinct sub-lineages corresponding to different survey locations. The characterization of A. rugioperculatus and P. bondari is essential for their management in coconut plantations. DNA barcoding and COI gene sequencing ensure accurate identification, while phylogenetic analysis reveals their invasion pathways and genetic diversity.