Root-knot nematodes of the genus Meloidogyne are obligatory plant endoparasites that threaten the global food supply. The most used non-chemical control method consists in deploying plant- resistant genes against Meloidogyne species. However, most resistance genes of cultivated plants in Europe are inefficient against Meloidogyne enterolobii which has been classified as a quarantine species this year. To gain insight into the molecular characteristics underlying its parasitic success, it is essential to explore the genomic plasticity of Meloidogyne enterolobii. In this study, we have produced PacBio high-fidelity long-read genome data for different geographical isolates of M. enterolobii that differ in their ranges of compatible hosts. Using the gap-aware sequence transformer, DeepConsensus, we have further improved reads quality and assembled the genomes of each isolate. We selected as a reference genome, the assembly that returned the best contiguity, which yielded a 273 Mbp genome with 556 contigs and an N50 value of 2.11Mb, the highest so far for a root-knot nematode. Combined analysis of k-mers and distribution of gene copies indicate the genome is triploid with diverged copies. We aligned PacBio Hi-Fi long reads from the different isolates to the reference genome to detect and genotype genomic structural variants (SVs) and propose a framework for the detection of SVs in complex organisms. We found on average 7053 SVs per sample spanning 2.96% of the reference genome. The most represented are deletions (56%) and insertions (38%). We will next investigate whether SVs patterns correlate with differences in the ranges of compatible hosts and geographical distribution.