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Bacterial endosymbionts, in genera <i>Wolbachia</i> and <i>Cardinium</i>, infect various arthropods and some nematode groups. Manipulating these microbial symbionts presents a promising biocontrol strategy for managing disease-causing parasites. However, the diversity of <i>Wolbachia</i> and <i>Cardinium</i> in nematodes remains unclear. This study employed a genome skimming strategy to uncover their occurrence in plant-parasitic nematodes, analyzing 52 populations of 12 species. A metagenome analysis revealed varying endosymbiont genome content, leading to the categorization of strong, weak, and no evidence for endosymbiont genomes. Strong evidence for <i>Wolbachia</i> was found in five populations, and for <i>Cardinium</i> in one population, suggesting a limited occurrence. Strong <i>Wolbachia</i> evidence was noted in <i>Pratylenchus penetrans</i> and <i>Radopholus similis</i> from North/South America and Africa. <i>Heterodera glycines</i> from North America showed strong <i>Cardinium</i> evidence. Weak genomic evidence for <i>Wolbachia</i> was observed in <i>Globodera pallida</i>, <i>Meloidogyne incognita</i>, <i>Rotylenchus reniformis</i>, <i>Pratylechus coffeae</i>, <i>Pratylenchus neglectus</i>, and <i>Pratylenchus thornei</i>; for <i>Cardinium</i> was found in <i>G. pallida</i>, <i>R. reniformis</i> and <i>P. neglectus</i>; 27/52 populations exhibited no endosymbiont evidence. <i>Wolbachia</i> and <i>Cardinium</i> presence varied within nematode species, suggesting non-obligate mutualism. <i>Wolbachia</i> and <i>Cardinium</i> genomes differed among nematode species, indicating potential species-specific functionality. This study advances knowledge of plant-parasitic nematode–bacteria symbiosis, providing insights for downstream eco-friendly biocontrol strategies.