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Here we report the discovery of a novel Sediminibacterium sequenced from laboratory cultures of freshwater stream cyanobacteria from sites in Southern California, grown in BG11 media. A de novo genome assembly of this bacterium yielded a complete chromosomal genome on a single contig of length 3.34 Mbps with a GC content of 39.4%. A first pass annotation identified ~3000 protein coding genes, with 98% completeness when compared against all prokaryotic and cyanobacterial gene families in BUSCO. A comprehensive phylogenomic species tree reconstruction using 100 of these protein coding genes placed the novel bacterium to be sister to a previously identified Sediminibacterium, which is over 20% divergent from our novel genome.