Among the root-knot nematodes three <i>Meloidogyne</i> species namely <i>Meloidogyne incognita, M. javanica</i>, and <i>M. arenaria</i> are emerging as an important pest of many cultivated plants, and recognized as the most economically destructive plant parasitic nematodes species of all over the world. Although other root-knot nematodes may virulent for plant but limited information is available. Thus, a comprehensive bioinformatics analysis including sequence acquisition, multiple sequence alignment and the phylogenetic tree construction for well-known <i>Meloidogyne</i> species was employed to predict the emerging virulent species. About eighty seven (87) 18S rRNA sequences of three damaging <i>Meloidogyne</i> species (<i>M. javanica, M. arenaria</i> and <i>M. incognita</i>) were retrieved from NCBI database, and allowed to construct phylogenetic trees using both NJ and ME methods of Molecular Evolution Genetic Analysis (MEGA) tools. Phylogeny analysis revealed that <i>M. enterolobii_1, M. sp._Mi_c3a, M. sp_Mj_c1a</i> and <i>M._sp._Mj_c3a</i> are genetically as well as evolutionally related to existing well recognized virulent nematodes. Moreover, evolutionally emerging strains of existing virulent species of <i>M. javanica, M. arenaria</i> and <i>M. incognita</i> along with the predicted virulence nematodes could become a great challenge to agriculture. The study could initiate the further analysis for novel insights in the pathogenesis of emerging virulence species of <i>Meloidogyne</i> that must be needed for future crop management strategies.