The study of membrane proteins and membrane protein complexes (MPC) provides crucial information in the field of bacterial physiology and pathogenesis research. The method of blue native polyacrylamide gel electrophoresis and its combination with SDS-PAGE (BN/SDS-PAGE) were here employed to study the membrane complexome of an intracellular bacterium Francisella tularensis, the causative agent of a severe disease tularemia. In the presented study we describe the subunit composition and stoichiometry of several MPC involved in various cell functions (oxidative phosphorylation, membrane transport, cell division, membrane or periplasmic proteins folding, iron storage, phospholipid and cell envelope biosynthesis). Moreover, some undocumented or hypothetical MPC with possible connection to virulence factors were also proposed and some newly detected subunits were assigned to known complexes. The BN/SDS-PAGE combined with mass spectrometry appeared to be a strong tool in the investigation of membrane proteins and complexes and thus successfully complements the traditional electrophoresis approaches.