Here we assemble a high-quality chromosome-level genome of M. rosenbergii by an integration of Nanopore, Illumina, and high-throughput chromosome conformation capture (Hi-C) sequencing technologies. Approximately 3.13 Gb (98.6%) of assembled sequences were anchored to 59 pseudo-chromosomes. The genome size is 3.18 Gb with a scaffold N50 of 62.73 Mb. A total of 17,436 protein-coding genes were annotated. Benchmarking Universal Single-Copy Orthologs (BUSCO) evaluation result showed that the final assembly was benchmarked at 94.5% and the annotation reached 91%.