diff --git a/hudi-client/hudi-spark-client/src/main/java/org/apache/hudi/table/action/bootstrap/SparkBootstrapCommitActionExecutor.java b/hudi-client/hudi-spark-client/src/main/java/org/apache/hudi/table/action/bootstrap/SparkBootstrapCommitActionExecutor.java
index 8b353d64c4f5a..3c876e75c28f5 100644
--- a/hudi-client/hudi-spark-client/src/main/java/org/apache/hudi/table/action/bootstrap/SparkBootstrapCommitActionExecutor.java
+++ b/hudi-client/hudi-spark-client/src/main/java/org/apache/hudi/table/action/bootstrap/SparkBootstrapCommitActionExecutor.java
@@ -77,6 +77,7 @@
 import org.apache.avro.generic.IndexedRecord;
 import org.apache.hadoop.fs.FileSystem;
 import org.apache.hadoop.fs.Path;
+import org.apache.hudi.table.marker.WriteMarkersFactory;
 import org.apache.log4j.LogManager;
 import org.apache.log4j.Logger;
 import org.apache.parquet.avro.AvroParquetReader;
@@ -144,6 +145,9 @@ public HoodieBootstrapWriteMetadata execute() {
       Option<HoodieWriteMetadata> metadataResult = metadataBootstrap(partitionSelections.get(BootstrapMode.METADATA_ONLY));
       // if there are full bootstrap to be performed, perform that too
       Option<HoodieWriteMetadata> fullBootstrapResult = fullBootstrap(partitionSelections.get(BootstrapMode.FULL_RECORD));
+      // Delete the marker directory for the instant
+      WriteMarkersFactory.get(config.getMarkersType(), table, instantTime)
+          .quietDeleteMarkerDir(context, config.getMarkersDeleteParallelism());
       return new HoodieBootstrapWriteMetadata(metadataResult, fullBootstrapResult);
     } catch (IOException ioe) {
       throw new HoodieIOException(ioe.getMessage(), ioe);
diff --git a/hudi-spark-datasource/hudi-spark/src/test/scala/org/apache/hudi/functional/TestDataSourceForBootstrap.scala b/hudi-spark-datasource/hudi-spark/src/test/scala/org/apache/hudi/functional/TestDataSourceForBootstrap.scala
index a4c98665ebdba..eeed5fe75b84a 100644
--- a/hudi-spark-datasource/hudi-spark/src/test/scala/org/apache/hudi/functional/TestDataSourceForBootstrap.scala
+++ b/hudi-spark-datasource/hudi-spark/src/test/scala/org/apache/hudi/functional/TestDataSourceForBootstrap.scala
@@ -17,7 +17,7 @@
 
 package org.apache.hudi.functional
 
-import org.apache.hadoop.fs.FileSystem
+import org.apache.hadoop.fs.{FileSystem, Path}
 import org.apache.hudi.bootstrap.SparkParquetBootstrapDataProvider
 import org.apache.hudi.client.bootstrap.selector.FullRecordBootstrapModeSelector
 import org.apache.hudi.common.fs.FSUtils
@@ -31,9 +31,9 @@ import org.apache.spark.sql.{SaveMode, SparkSession}
 import org.junit.jupiter.api.Assertions.assertEquals
 import org.junit.jupiter.api.io.TempDir
 import org.junit.jupiter.api.{AfterEach, BeforeEach, Test}
-
 import java.time.Instant
 import java.util.Collections
+
 import scala.collection.JavaConverters._
 
 class TestDataSourceForBootstrap {
@@ -106,6 +106,8 @@ class TestDataSourceForBootstrap {
       DataSourceWriteOptions.COW_TABLE_TYPE_OPT_VAL,
       extraOpts = Map(DataSourceWriteOptions.KEYGENERATOR_CLASS_NAME.key -> "org.apache.hudi.keygen.NonpartitionedKeyGenerator")
     )
+    // check marked directory clean up
+    assert(!fs.exists(new Path(basePath, ".hoodie/.temp/00000000000001")))
 
     // Read bootstrapped table and verify count
     var hoodieROViewDF1 = spark.read.format("hudi").load(basePath + "/*")
@@ -161,6 +163,9 @@ class TestDataSourceForBootstrap {
       Some("datestr"),
       Map(DataSourceWriteOptions.HIVE_STYLE_PARTITIONING.key -> "true"))
 
+    // check marked directory clean up
+    assert(!fs.exists(new Path(basePath, ".hoodie/.temp/00000000000001")))
+
     // Read bootstrapped table and verify count
     val hoodieROViewDF1 = spark.read.format("hudi").load(basePath + "/*")
     assertEquals(numRecords, hoodieROViewDF1.count())