Thermotoga neapolitana is a hyperthermophilic eubacterium that produces hydrogen by sugar fermentation. A lab strain of T. neapolitana DSMZ 4359T maintained in a CO2-enriched atmosphere showed a stable increase of lactic acid production under capnophilic lactic fermentation (CLF) conditions. The genotypic comparison between the putative mutant (TN-CMut) and the original strain DSMZ 4359T (WT4359) revealed 88.1 (±2.4)% DNA homology. RiboPrint® and MALDI-TOF mass analyses support a genetic differentiation beyond subspecies level. The phenotypic characterization indicated a high correlation between the two strains, except for the lactic acid production. Under identical operating conditions, the lab mutant produced significantly more lactic acid than the parent strain without impairing the hydrogen yield. The highest divergence between TN-CMut and WT4359 was observed for fermentation of glucose or lactose at 80 °C. Based on these results, we propose that the lab strain is a new subspecies of the genus Thermotoga that is named T. neapolitana subsp. capnolactica with regards to its improved feature to produce lactic acid under capnophilic conditions.