The crystal structures of 23 samples extracted from a large slice oriented along (001) of a single crystal of liddicoatite from the Anjanabonoina granitic pegmatite in Madagascar (showing pronounced, visually discontinuous oscillatory zones and anomalous biaxiality) were refined to R1 indices of 1.5–2.9% (<R1> = 1.78%). Cell parameters are in the range a ≈ 15.82–15.87, c ≈ 7.10–7.12 Å. Spindle-stage measurement of 2V gave values of 0.0° for a fragment from the (001) zone and 8(3) and 18.9(5)° for fragments from the pyramidal zone of the crystal. However, single-crystal X-ray intensity data show no deviation from 3m Laue symmetry, indicating that there is no information in the diffraction data on any deviation from R3m symmetry. The <T–O> distances are in the range 1.616–1.619 Å, with a grand mean value of 1.6175(7) Å. The occupancy of the T site was expressed as xSi + (1−x)B, and x was treated as variable in the refinement procedure. The effect of using different scattering factors (i.e., ionized versus neutral) on the refined site-occupancies was investigated in detail. The grand mean refined B content of the T site varies from −0.04 apfu for ionized scattering-curves for O and Si to 0.25 apfu for neutral scattering-curves for O and Si, illustrating the effect of the use of different scattering curves on refined B site-populations. Examination of <T–O> distances as a function of aggregate cation radius for tourmalines containing B and Al shows a large amount of scatter, emphasizing the need for more accurate data. The limits of detection for 11B and 27Al in tourmaline by Magic-Angle-Spinning Nuclear Magnetic Resonance (MAS NMR) spectroscopy were investigated by simulation. For minimum (<0.04 apfu) and maximum (0.12 apfu) contents of (paramagnetic) transition metals, the limits of detection of B are~0.02 and 0.08 apfu, and of Al are~0.01 and 0.01 apfu, respectively. 11B and 27Al MAS NMR spectroscopy gave no evidence of the presence of tetrahedrally coordinated B or Al at the T site above these detection limits in any sample. This result is in accord with our refinement results using an ionized scattering-curve for O and a neutral scattering-curve for Si, suggesting that use of these curves is giving more accurate results than refinement with neutral scattering factors. The <Z–O> distances are in the range 1.904–1.907 Å, with a grand mean value of 1.9047(8) Å, and structure refinement indicates site-scattering values in accord with complete occupancy of the Z site by Al. Hence throughout this complexly zoned crystal, Si = 6.00 apfu and ZAl = 6.00 apfu.