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Bacteria of the genera <i>Xenorhabdus</i> and <i>Photorhabdus</i> are symbionts of entomopathogenic nematodes. Despite their close phylogenetic relationship, they show differences in their pathogenicity and virulence mechanisms in target insects. These differences were explored by the analysis of the pangenome, as it provides a framework for characterizing and defining the gene repertoire. We performed the first pangenome analysis of 91 strains of <i>Xenorhabdus</i> and <i>Photorhabdus</i>; the analysis showed that the <i>Photorhabdus</i> genus has a higher number of genes associated with pathogenicity. However, biological tests showed that whole cells of <i>X. nematophila</i> SC 0516 were more virulent than those of <i>P. luminescens</i> HIM3 when both were injected into <i>G. mellonella</i> larvae. In addition, we cloned and expressed the GroEL proteins of both bacteria, as this protein has been previously indicated to show insecticidal activity in the genus <i>Xenorhabdus</i>. Among these proteins, Cpn60-Xn was found to be the most toxic at all concentrations tested, with an LC50 value of 102.34 ng/larva. Sequence analysis suggested that the Cpn60-Xn toxin was homologous to Cpn60-Pl; however, Cpn60-Xn contained thirty-five differentially substituted amino acid residues that could be responsible for its insecticidal activity.