<P><B>Background</B></P><P>The overreliance on dwindling fossil fuel reserves and the negative climatic effects of using such fuels are driving the development of new clean energy sources. One such alternative source is hydrogen (H<SUB>2</SUB>), which can be generated from renewable sources. <I>Parageobacillus thermoglucosidasius</I> is a facultative anaerobic thermophilic bacterium which is frequently isolated from high temperature environments including hot springs and compost.</P><P><B>Results</B></P><P>Comparative genomics performed in the present study showed that <I>P. thermoglucosidasius</I> encodes two evolutionary distinct H<SUB>2</SUB>-uptake [Ni-Fe]-hydrogenases and one H<SUB>2</SUB>-evolving hydrogenases. In addition, genes encoding an anaerobic CO dehydrogenase (CODH) are co-localized with genes encoding a putative H<SUB>2</SUB>-evolving hydrogenase. The co-localized of CODH and uptake hydrogenase form an enzyme complex that might potentially be involved in catalyzing the water-gas shift reaction (CO + H<SUB>2</SUB>O → CO<SUB>2</SUB> + H<SUB>2</SUB>) in <I>P. thermoglucosidasius</I>. Cultivation of <I>P. thermoglucosidasius</I> DSM 2542<SUP>T</SUP> with an initial gas atmosphere of 50% CO and 50% air showed it to be capable of growth at elevated CO concentrations (50%). Furthermore, GC analyses showed that it was capable of producing hydrogen at an equimolar conversion with a final yield of 1.08 H<SUB>2</SUB>/CO.</P><P><B>Conclusions</B></P><P>This study highlights the potential of the facultative anaerobic <I>P. thermoglucosidasius</I> DSM 2542<SUP>T</SUP> for developing new strategies for the biohydrogen production.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (10.1186/s12934-018-0954-3) contains supplementary material, which is available to authorized users.</P>