Here, we report a new metagenome-assembled genome (MAG) from a marine Rhizobiaceae species. The MnEN-MB40S genome was assembled from a manganese-oxidizing enrichment culture metagenome. A 4.1-Mb MAG comprising 26 contigs, with a GC content of 60.0%, was obtained. This MAG contributes to the genomic information regarding the family Rhizobiaceae.