<p>The present study investigates the molecular characterization of <i>Thrips parvispinus</i>, an invasive pest species causing severe damage to chilli (<i>Capsicum annuum</i>) crops in southern India, and its association with the endosymbiotic bacterium <i>Wolbachia</i>. The study aims to elucidate the genetic diversity of <i>T. parvispinus</i>, assess its symbiotic interactions, and explore the ecological implications of these relationships to support the development of sustainable pest management strategies. Comprehensive field surveys conducted in Karnataka confirmed the widespread dominance of <i>T. parvispinus</i> on chilli plants, underscoring its rapid proliferation and economic significance in these areas. Specimens underwent morphological identification and molecular characterization using the mitochondrial cytochrome oxidase I (<i>mt</i>COI) and nuclear 18S ribosomal RNA genes, which highlighted significant genetic variation and the phylogeny confirmed the authenticity of the sequences and provided insights into the evolutionary relationships among <i>T. parvispinus</i> populations, shedding light on its genetic structure and invasive potential. Further analysis also confirmed a high prevalence of <i>Wolbachia</i> endosymbionts in the <i>T. parvispinus</i> populations, suggesting a role for this bacterium within <i>T. parvispinus</i> populations. Phylogenetic studies of <i>Wolbachia</i> reveal close genetic relationships with other <i>Wolbachia</i> strains, indicating potential co-evolution or horizontal gene transfer. These findings provide new insights into thrips'genetic diversity and the symbiotic relationships that may enhance their adaptability, supporting future pest management approaches targeting <i>Wolbachia</i> to control <i>T. parvispinus</i>.</p>