diff --git a/image_analysis/rotation_indexer/RotationIndexer.cpp b/image_analysis/rotation_indexer/RotationIndexer.cpp
index 540fe022..355e5b00 100644
--- a/image_analysis/rotation_indexer/RotationIndexer.cpp
+++ b/image_analysis/rotation_indexer/RotationIndexer.cpp
@@ -12,6 +12,14 @@
 #include <future>
 
 namespace {
+    // Sub-cell override thresholds used in candidate selection to undo a spurious axis doubling:
+    // a later candidate replaces the chosen cell when it is smaller by more than this volume ratio
+    // (a doubling is 2x, well past 1.5) and indexes within this fraction slack of it. The slack is
+    // far below the indexed-fraction gap a real superstructure opens between its true cell and its
+    // sub-cell, so genuine large cells are kept.
+    constexpr float ROT_SUBCELL_VOLUME_RATIO = 1.5f;
+    constexpr float ROT_SUBCELL_FRAC_SLACK = 0.02f;
+
     // Re-express a primitive hexagonal/trigonal lattice in the conventional hexagonal setting
     // (a = b, gamma = 120). The Niggli-reduced primitive cell carries the two equal-length axes
     // at gamma = 60; replacing b with b - a opens that angle to 120 without changing the lattice.
@@ -224,6 +232,7 @@ void RotationIndexer::RunIndexing() {
 
         // Assemble and select serially, in candidate order - identical to refining them one by one.
         float best_frac = -1.0f;
+        float best_vol = 0.0f;
         bool have_best = false;
         size_t best_ci = 0;
         XtalOptimizerData best_data;
@@ -264,8 +273,21 @@ void RotationIndexer::RunIndexing() {
             // marginally-higher alternative from displacing the primary when both index poorly (e.g. a
             // twin, where the accumulated-spot fraction is a noisy proxy) - only a decisively better
             // cell (a superstructure's true cell vs its sublattice) takes over.
-            if (!have_best || (frac > best_frac + 0.05f && frac > 0.15f)) {
+            // Displace the current best when the candidate indexes clearly more, OR when it is a
+            // genuine sub-cell: a meaningfully smaller cell that still indexes at least as many spots.
+            // The sub-cell branch unmasks a spurious supercell (axis doubling): the primitive cell
+            // always indexes >= its integer multiple, so a doubled cell that wins ci-order by the
+            // hysteresis margin is overridden by its own primitive. A real superstructure's true
+            // (larger) cell indexes MORE than its sub-cell and is kept by the clearly-more branch;
+            // twin lattices share the cell volume, so this never disturbs twin selection.
+            const float cand_vol = std::abs(data.latt.CalcVolume());
+            const bool clearly_more = frac > best_frac + 0.05f && frac > 0.15f;
+            const bool smaller_subcell = have_best && frac > 0.15f
+                                         && frac >= best_frac - ROT_SUBCELL_FRAC_SLACK
+                                         && cand_vol < best_vol / ROT_SUBCELL_VOLUME_RATIO;
+            if (!have_best || clearly_more || smaller_subcell) {
                 best_frac = frac;
+                best_vol = cand_vol;
                 have_best = true;
                 best_data = std::move(data);
                 best_sr = sr;