The genome assembly of Magnetominusculus dajiuhuensis is of high quality, as indicated by the completeness score of 99.09% and the low contamination rate of 1.82%. The presence of all key ribosomal RNA genes (1 copy each of 16S, 23S, and 5S rRNA genes), 19 tRNA genes and a substantial number of coding sequences (3,368 CDS) indicates a functionally complete genome. The N50 value of 23,014 bp and the significant length of the largest contig (101,549 bp) also suggest that many parts of the genome are well-assembled and thus it can prove to be a valuable resource for further studies on this organism.