Type genome is Fontibacterium baikalense Baikal-deep-G36 (GCA_009693745.1), a metagenome-assembled genome (MAG) co-assembled from 1250 m and 1350 m depth from Lake Baikal, Russia (date: 2018-03-29). Baikal-deep-G36 has a genome size of 1 Mbp with a genomic GC content of 29.4%, contains 2 rRNA genes and 25 tRNAs. The genome is of high quality, consisting of 66 contigs, with a completeness of 95.2%, contamination of 3.9% and strain heterogeneity of 100% as assessed with checkM. The metagenome was assembled with IDBA-UD assembler from short-read sequencing (Illumina HiSeq 3000/4000). The closest cultivated relatives are Fontibacterium commune, syn. ‘Candidatus Fonsibacter ubiquis’ LSUCC0530 (GCF_002688585.1; later reclassified to ‘Ca. Allofontibacter communis’), with an average amino acid identity of 85.75% and average nucleotide identity of 84.65% and another newly proposed species, Fontibacterium medardicus ME-17, with an AAI of 88.73% and an ANI of 87.93%. Current GTDB classification (R220): d__Bacteria; p__Pseudomonadota; c__Alphaproteobacteria; o__Pelagibacterales; f__Pelagibacteraceae; g__Fonsibacter; s__Fonsibacter sp009693745.