The Neotropical palm infesting whitefly, Aleurotrachelus atratus Hempel (Hemiptera: Aleyrodidae) is a highly invasive pest that was reported during 2019 on coconut in India. In a short span of time, it spread rapidly across states of Karnataka, Tamil Nadu, Kerala and Andhra Pradesh on coconut, oil palm and many other ornamental palm plants. During the recent survey, the immature stages of A. atratus were found parasitized by an aphelinid parasitoid, Encarsia cubensis Gahan (Hymenoptera: Aphelinidae). These parasitoids were identified by their morphological characteristics and also characterized by DNA barcoding of adult parasitoids using partial (658 bp) mitochondrial cytochrome oxidase 1 (CO1) gene (GenBank accession number ON881119). This is the first report on occurrence of Encarsia cubensis as primary parasitoids on A. atratus in India and its natural parasitism ranged from (46–68%) on coconut across the different locations in Karnataka. It is believed that the parasitoid likely entered India along with A. atratus in India and constitutes a potential biological agent against A. atratus. It is expected that the E. cubensis population will become fully established, increase, spread and exert a significant impact on A. atratus population in India. Therefore, efforts may be made by growers and other stakeholders to increase the rate of natural parasitism through inundative, conservation and classical biological control approaches to reduce the pest population, crop damage and yield loss.