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We present the chromosome-scale genome assembly of the allopolyploid root-knot nematode Meloidogyne javanica. We show that the M. javanica genome is predominantly allotetraploid, comprising two subgenomes, A and B, that most likely originated from hybridisation of two ancestral parental species. The assembly was annotated using full-length non-chimeric transcripts, comparison to reference databases, and ab initio prediction techniques, and the subgenomes were phased using ancestral k-mer spectral analysis. Subgenome B appears to show fission of chromosomal contigs, and while there is substantial synteny between subgenomes, we also identified regions lacking synteny that may have diverged in the ancestral genomes prior to or following hybridisation. This annotated and phased genome assembly forms a significant resource for understanding the origins and genetics of these globally important plant pathogens. Author summary: Root-knot nematodes represent one of the most significant crop parasites globally. Despite their agricultural importance, only limited genomic resources have been published to date, leaving a gap in the understanding of genetic mechanisms driving genome evolution and crop virulence. Here, we have used modern genomic and bioinformatic approaches to create a chromosome-scale reference assembly to investigate the origins and genomic composition of the root-knot nematode species Meloidogyne javanica. This species has an allopolyploid genome, reproduces by ameiotic parthenogenesis and is among the most damaging plant parasitic nematodes with a large and expanding plant host range. Utilising modern long-read DNA sequencing and bioinformatics approaches, we successfully phased the assembly into its constituent subgenomes, a first for this agriculturally important clade. While we find the genomic landscape is mostly syntenic between subgenomes, we identified regions of minimal similarity, and highlight structural divergence between subgenomes. [ABSTRACT FROM AUTHOR]