Root-knot nematodes of the genus Meloidogyne are obligatory plant endoparasites that threaten the global food supply. The preferred non-chemical control method consists in deploy- ing plant-resistant genes against Meloidogyne species. However, most European vegetable plant resistance genes are inefficient against M. enterolobii, which was recently declared a quarantine pest. To unravel the molecular characteristics underlying its parasitic success, a thorough ex- ploration of the genomic plasticity of M. enterolobii is essential. In this study, we report PacBio high-fidelity long-read genome data for distinct geographical isolates of M. enterolobii, exhibiting different ranges of compatible hosts. Using the gap-aware sequence transformer, DeepConsen- sus, we have further improved reads quality and assembled each isolate genome. We selected as a reference genome, the assembly that returned the best contiguity, which yielded a 273 Mbp genome with 556 contigs and a N50 value of 2.11Mb, the highest so far for a polyploid partheno- genetic root-knot nematode at the contig level. Combined analysis of k-mers and distribution of gene copies indicate the genome is triploid with diverged AAB sub-genomes. By aligning PacBio Hi-Fi long reads from the different geographical isolates to the reference genome, we have de- tected and genotyped genomic structural variants (SVs). We also propose a novel framework for the detection of SVs in complex organisms. Our findings indicate 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.