Nanopore sequencing can obtain long reads, which help to overcome the challenges posed by AT- and repeat-rich genomes, such as those found in phytoplasmas. Additionally, removing short DNA fragments improves the read length distribution before sequencing. Here, we present a methodology for extracting genomic DNA from phytoplasma-infected plants, the removal of short DNA fragments under 10 kb, and utilizing nanopore sequencing to generate lengthy reads. Furthermore, we outline procedures for assembling a circular genome by removing the plant sequence and refining it using short reads generated by Illumina sequencing to correct sequencing errors.