Type strain is Limnohabitans simekii MiE-M12 (GCA_965234735.1), isolated from 5 m depth from Lake Milada, Czechia (date: 2019-04-16), via high-throughput dilution to extinction cultivation. MiE-M12 has a genome size of 2.7 Mbp with a genomic GC content of 55.8 %, contains 3 rRNA genes and 37 tRNAs. The genome is a high-quality draft consisting of 9 contigs. The genome contains genes encoding anoxygenic aerobic phototrophy (pufABLM) and the complete Calvin cycle for carbon fixation via RuBisCO. Genes for flagellar and pilus assembly were annotated. Pathways for urea degradation, thiosulfate oxidation (Sox pathway), glycolate oxidation, and the biosynthesis of all amino acids were predicted. Further, pathways for thiamine, riboflavin, coenzyme A, biotin, THF, and heme biosynthesis were identified. The closest cultivated relative is Limnohabitans sp. Jir61 (GCF_003063545.1) with an average amino acid identity of 66.2% and average nucleotide identity of 72.6%. Current GTDB classification (R220): d__Bacteria; p__Pseudomonadota; c__Gammaproteobacteria; o__Burkholderiales; f__Burkholderiaceae_B; g__Limnohabitans; s__Limnohabitans sp937891045.