diff --git a/rust/lance-index/src/scalar/btree.rs b/rust/lance-index/src/scalar/btree.rs
index 6d21e842e04..371be42126e 100644
--- a/rust/lance-index/src/scalar/btree.rs
+++ b/rust/lance-index/src/scalar/btree.rs
@@ -29,7 +29,8 @@ use crate::{metrics::NoOpMetricsCollector, scalar::registry::TrainingCriteria};
 use crate::{pbold, scalar::btree::flat::FlatIndex};
 use arrow_arith::numeric::add;
 use arrow_array::{
-    Array, ArrayAccessor, ArrowNativeTypeOp, PrimitiveArray, RecordBatch, UInt32Array,
+    Array, ArrayAccessor, ArrowNativeTypeOp, BooleanArray, PrimitiveArray, RecordBatch,
+    UInt32Array,
     cast::AsArray,
     new_empty_array,
     types::{
@@ -1856,7 +1857,8 @@ impl BTreeIndex {
                 ..Default::default()
             },
         )?;
-        let merged_stream = chunk_concat_stream(unchunked, first.batch_size as usize);
+        let deduplicated = deduplicate_value_ordered_btree_rows(unchunked);
+        let merged_stream = chunk_concat_stream(deduplicated, first.batch_size as usize);
 
         let files =
             train_btree_index(merged_stream, dest_store, first.batch_size, None, None).await?;
@@ -1889,6 +1891,51 @@ fn filter_row_ids(
     Box::pin(RecordBatchStreamAdapter::new(schema, filtered))
 }
 
+fn deduplicate_value_ordered_btree_rows(
+    stream: SendableRecordBatchStream,
+) -> SendableRecordBatchStream {
+    let schema = stream.schema();
+    let deduplicated = stream::try_unfold(
+        (stream, None::<ScalarValue>, HashSet::<u64>::new()),
+        |(mut stream, mut current_value, mut row_ids_for_value)| async move {
+            loop {
+                let Some(batch) = stream.next().await.transpose()? else {
+                    return Ok(None);
+                };
+
+                let values = batch.column_by_name(VALUE_COLUMN_NAME).expect_ok()?;
+                let row_ids = batch
+                    .column_by_name(ROW_ID)
+                    .expect_ok()?
+                    .as_primitive::<UInt64Type>();
+                let mut mask = Vec::with_capacity(batch.num_rows());
+
+                for idx in 0..batch.num_rows() {
+                    let value = ScalarValue::try_from_array(values, idx)?;
+                    match current_value.as_ref() {
+                        Some(current)
+                            if OrderableScalarValue(current.clone())
+                                .cmp(&OrderableScalarValue(value.clone()))
+                                == Ordering::Equal => {}
+                        _ => {
+                            current_value = Some(value);
+                            row_ids_for_value.clear();
+                        }
+                    }
+                    mask.push(row_ids_for_value.insert(row_ids.value(idx)));
+                }
+
+                let mask = BooleanArray::from(mask);
+                let batch = arrow_select::filter::filter_record_batch(&batch, &mask)?;
+                if batch.num_rows() > 0 {
+                    return Ok(Some((batch, (stream, current_value, row_ids_for_value))));
+                }
+            }
+        },
+    );
+    Box::pin(RecordBatchStreamAdapter::new(schema, deduplicated))
+}
+
 fn wrap_bound(bound: &Bound<ScalarValue>) -> Bound<OrderableScalarValue> {
     match bound {
         Bound::Unbounded => Bound::Unbounded,
diff --git a/rust/lance/src/dataset/tests/dataset_merge_update.rs b/rust/lance/src/dataset/tests/dataset_merge_update.rs
index 7fa03d6e78d..0660e5afcba 100644
--- a/rust/lance/src/dataset/tests/dataset_merge_update.rs
+++ b/rust/lance/src/dataset/tests/dataset_merge_update.rs
@@ -1626,6 +1626,63 @@ async fn test_merge_insert_with_reordered_columns_and_index() {
     final_dataset.validate().await.unwrap();
 }
 
+#[tokio::test]
+async fn test_btree_merge_deduplicates_row_addrs() {
+    // This public table flow creates an old BTree segment and a delta segment
+    // for the same row address. Merging them should not leave duplicate row
+    // addresses in the final flat page.
+    let batch = arrow_array::record_batch!(("id", Int32, [1]), ("payload", Int32, [10])).unwrap();
+    let test_uri = TempStrDir::default();
+    let reader = RecordBatchIterator::new(vec![Ok(batch.clone())], batch.schema());
+    let mut dataset = Dataset::write(reader, &test_uri, None).await.unwrap();
+
+    dataset
+        .create_index(
+            &["id"],
+            IndexType::BTree,
+            None,
+            &ScalarIndexParams::default(),
+            false,
+        )
+        .await
+        .unwrap();
+
+    let source_batch =
+        arrow_array::record_batch!(("payload", Int32, [100]), ("id", Int32, [1])).unwrap();
+    let merge_job = MergeInsertBuilder::try_new(Arc::new(dataset.clone()), vec!["id".to_string()])
+        .unwrap()
+        .when_matched(WhenMatched::UpdateAll)
+        .try_build()
+        .unwrap();
+    let reader = Box::new(RecordBatchIterator::new(
+        vec![Ok(source_batch.clone())],
+        source_batch.schema(),
+    ));
+    let (updated_dataset, _) = merge_job.execute(reader_to_stream(reader)).await.unwrap();
+    let mut dataset = updated_dataset.as_ref().clone();
+
+    dataset
+        .optimize_indices(&OptimizeOptions::append())
+        .await
+        .unwrap();
+    dataset
+        .optimize_indices(&OptimizeOptions::merge(2))
+        .await
+        .unwrap();
+
+    let actual = dataset
+        .scan()
+        .filter("id = 1")
+        .unwrap()
+        .try_into_batch()
+        .await
+        .unwrap();
+
+    assert_eq!(actual.num_rows(), 1);
+    assert_eq!(actual["id"].as_primitive::<Int32Type>().value(0), 1);
+    assert_eq!(actual["payload"].as_primitive::<Int32Type>().value(0), 100);
+}
+
 /// DataReplacement should invalidate index fragment bitmaps for replaced fields.
 #[tokio::test]
 async fn test_data_replacement_invalidates_index_bitmap() {