The structure of an intermediate scapolite (Me36.6) from Lake Clear, Ontario, was obtained using synchrotron high-resolution powder X-ray diffraction (HRPXRD) data and Rietveld structure refinement in space group P42/n. The chemical formula obtained by electron microprobe is Na2.19Ca1.35K0.16[Al3.95Si8.05O24]Cl0.55(CO3)0.41(SO4)0.04, equivalent to Me36.6. The unit-cell parameters are a 12.07899(1), c 7.583467(9) Å, and V 1106.443(2) Å3. The average distances are <T1–O> = 1.617(1) Å, <T2–O> = 1.744(1) Å, and <T3–O> = 1.601(1) Å. Therefore, the T1 and T3 sites contain only Si atoms, and the T2 site contains only Al atoms, so the Al and Si atoms are completely ordered. Complete Al–Si order was predicted for Me37.5, ideally Ca3Na5[Al8Si16O48]Cl(CO3), and is confirmed in this study. Antiphase domain boundaries (APBs) in scapolite cannot arise from Al–Si order because the average <T–O> distances indicate complete Al–Si order in Me36.6. If APBs were to arise from Al–Si order, switching of the T sites across the APBs will occur, and complete Al–Si order cannot be observed. Therefore, Al–Si order, which is present to various extents across the scapolite series, can be ruled out as the cause for the APBs. Order involving Cl and CO3 is the cause for the APBs in scapolite.