Root-knot nematodes (RKN; genus Meloidogyne) are polyphagous plant pathogens of great economic importance to agriculturalists globally . These species are small, diverse, and can be challenging for accurate taxonomic identification . Many of the most important crop pests confound analysis with simple genetic marker loci as they are polyploids of likely hybrid origin . Here we take a low-coverage, long-read genome sequencing approach to characterisation of individual root-knot nematodes . We demonstrate library preparation for Oxford Nanopore Technologies Flongle sequencing of low input DNA from individual juveniles and immature females, multiplexing up to twelve samples per flow cell . Taxonomic identification with Kraken 2 (a k-mer-based taxonomic assignment tool) is shown to reliably identify individual nematodes to species level, even within the very closely related Meloidogyne incognita group . Our approach forms a robust, low-cost, and scalable method for accurate RKN species diagnostics.