Type strain is Hydrogenophaga miladensis MiE-M28 (GCA_965234585.1), isolated from 5 m depth from Lake Milada, Czechia (date: 2019-10-15), via high-throughput dilution to extinction cultivation. MiE-M28 has a genome size of 2.4 Mbp with a genomic GC content of 60.6%, contains 6 rRNA genes and 43 tRNAs. The genome is complete, consisting of a circular chromosome. 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 thiosulfate oxidation (Sox pathway), glycolate and methane/alkanesulfonate oxidation and the biosynthesis of all amino acids were predicted. Further, pathways for thiamine, riboflavin, NAD, coenzyme A, pimeloyl-ACP, and heme biosynthesis were identified. The closest cultivated relative is Hydrogenophaga intermedia MER 62 (GCF_001571205.1), with an average nucleotide identity of 74.2%. Current GTDB classification (R220): d__Bacteria; p__Pseudomonadota; c__Gammaproteobacteria; o__Burkholderiales; f__Burkholderiaceae_B; g__Hydrogenophaga; s__Hydrogenophaga intermedia_C.