diff --git a/gtsam/hybrid/HybridBayesNet.cpp b/gtsam/hybrid/HybridBayesNet.cpp
index 163e77e47..96a6dfd63 100644
--- a/gtsam/hybrid/HybridBayesNet.cpp
+++ b/gtsam/hybrid/HybridBayesNet.cpp
@@ -70,12 +70,37 @@ PrunerFunc(const DecisionTreeFactor::shared_ptr &probDecisionTree,
     // typecast so we can use this to get probability value
     DiscreteValues values(choices);
 
-    if ((*probDecisionTree)(values) == 0.0) {
-      // empty aka null pointer
-      boost::shared_ptr<GaussianConditional> null;
-      return null;
+    // Case where the gaussian mixture has the same
+    // discrete keys as the decision tree.
+    if (gaussianMixtureKeySet == discreteFactorKeySet) {
+      if ((*probDecisionTree)(values) == 0.0) {
+        // empty aka null pointer
+        boost::shared_ptr<GaussianConditional> null;
+        return null;
+      } else {
+        return conditional;
+      }
     } else {
-      return conditional;
+      std::vector<DiscreteKey> set_diff;
+      std::set_difference(
+          discreteFactorKeySet.begin(), discreteFactorKeySet.end(),
+          gaussianMixtureKeySet.begin(), gaussianMixtureKeySet.end(),
+          std::back_inserter(set_diff));
+      const std::vector<DiscreteValues> assignments =
+          DiscreteValues::CartesianProduct(set_diff);
+      for (const DiscreteValues &assignment : assignments) {
+        DiscreteValues augmented_values(values);
+        augmented_values.insert(assignment.begin(), assignment.end());
+
+        // If any one of the sub-branches are non-zero,
+        // we need this conditional.
+        if ((*probDecisionTree)(augmented_values) > 0.0) {
+          return conditional;
+        }
+      }
+      // If we are here, it means that all the sub-branches are 0,
+      // so we prune.
+      return nullptr;
     }
   };
   return pruner;
@@ -112,12 +137,6 @@ HybridBayesNet HybridBayesNet::prune(size_t maxNrLeaves) const {
       // We may have mixtures with less discrete keys than discreteFactor so
       // we skip those since the label assignment does not exist.
       auto gmKeySet = DiscreteKeysAsSet(gaussianMixture->discreteKeys());
-      if (gmKeySet != discreteFactorKeySet) {
-        // Add the gaussianMixture which doesn't have to be pruned.
-        prunedBayesNetFragment.push_back(
-            boost::make_shared<HybridConditional>(gaussianMixture));
-        continue;
-      }
 
       // Get the pruner function.
       auto pruner = PrunerFunc(discreteFactor, discreteFactorKeySet, gmKeySet);