In contrast to other prokaryotes, the Mycobacterial FF ATP synthase (α:β:γ:δ:ε:a:b:b':c) is essential for growth. The mycobacterial enzyme is also unique as a result of its 111 amino acids extended δ subunit, whose gene is fused to the peripheral stalk subunit b. Recently, the crystallographic structures of the mycobacterial α:β:γ:ε-domain and c subunit ring were resolved. Here, we report the first purification protocol of the intact M. smegmatis FF ATP synthase including the F-domain, the entire membrane-embedded F sector, and the stator subunits b' and the fused b-δ. This enzyme purification enabled the determination of the first projected 2D- and 3D structure of the intact M. smegmatis FF ATP synthase by electron microscopy (EM) and single particle analysis. Expression and purification of the fused mycobacterial b-δ construct, excluding the membrane-embedded N-terminal amino acids, provided insight into its secondary structure. By combining these data with homology and ab-initio modeling techniques, a model of the mycobacterial peripheral stalk subunits b-δ and b' was generated. Superposition of the 3D M. smegmatis F-ATP synthase EM-structure, the α:β:γ:ε and c-ring, and the derived structural models of the peripheral stalk enabled a clear assignment of all F-ATP synthase subunits, in particular with respect to the unique mycobacterial peripheral stalk subunit b' and the elongated δ fused with subunit b. The arrangement of δ relative to the N-termini of the catalytic αβ-headpiece and its potential as a drug target are discussed.