Madhya Pradesh, a biodiversity-rich state in central India, reports sporadic non-indigenous leishmaniasis cases. Systematic entomological surveillance as part of molecular xenomonitoring in sand flies led to the discovery of a new species, Sergentomyia (Neophlebotomus) pradeepii n. sp. (Diptera: Psychodidae), from Johariya village in Sagar district, Madhya Pradesh, India. A systematic cross-sectional survey of sand flies was conducted in Bhopal, Sagar, and Hoshangabad districts of Madhya Pradesh. Standard collection methods were employed for two months, i.e., from July to August 2023. DNA barcoding targeting the mitochondrial Cytochrome c oxidase subunit I (COI) gene was performed, and the generated sequences were phylogenetically analyzed. Se. (Neo.) pradeepii, a newly recorded sand fly species, is reported in this study. Its taxonomic relationship to other congeners of subgenus Neophlebotomus is discussed. COI barcoding and phylogenetic analysis established that the specimens fit into the same taxonomic group, exhibiting negligible gene flow within the population, while a 13.4% genetic distance from congeners establishes it as a separate species. Madhya Pradesh, with its rich biodiversity and favorable conditions for sand fly proliferation, lacks systematic entomological surveillance. This study enhances the knowledge of the state’s sand fly fauna by reporting and providing a detailed morphological and molecular description of the new species.