diff --git a/src/dawn_native/CommandEncoder.cpp b/src/dawn_native/CommandEncoder.cpp
index 6d24609ef8..0fdded3f97 100644
--- a/src/dawn_native/CommandEncoder.cpp
+++ b/src/dawn_native/CommandEncoder.cpp
@@ -467,6 +467,24 @@ namespace dawn_native {
         mUsedQuerySets.insert(querySet);
     }
 
+    void CommandEncoder::TrackUsedQueryIndex(QuerySetBase* querySet, uint32_t queryIndex) {
+        UsedQueryMap::iterator it = mUsedQueryIndices.find(querySet);
+        if (it != mUsedQueryIndices.end()) {
+            // Record index on existing query set
+            std::vector<bool>& queryIndices = it->second;
+            queryIndices[queryIndex] = 1;
+        } else {
+            // Record index on new query set
+            std::vector<bool> queryIndices(querySet->GetQueryCount(), 0);
+            queryIndices[queryIndex] = 1;
+            mUsedQueryIndices.insert({querySet, std::move(queryIndices)});
+        }
+    }
+
+    const UsedQueryMap& CommandEncoder::GetUsedQueryIndices() const {
+        return mUsedQueryIndices;
+    }
+
     // Implementation of the API's command recording methods
 
     ComputePassEncoder* CommandEncoder::BeginComputePass(const ComputePassDescriptor* descriptor) {
@@ -850,10 +868,12 @@ namespace dawn_native {
         mEncodingContext.TryEncode(this, [&](CommandAllocator* allocator) -> MaybeError {
             if (GetDevice()->IsValidationEnabled()) {
                 DAWN_TRY(GetDevice()->ValidateObject(querySet));
-                DAWN_TRY(ValidateTimestampQuery(querySet, queryIndex));
+                DAWN_TRY(ValidateTimestampQuery(querySet, queryIndex, GetUsedQueryIndices()));
                 TrackUsedQuerySet(querySet);
             }
 
+            TrackUsedQueryIndex(querySet, queryIndex);
+
             WriteTimestampCmd* cmd =
                 allocator->Allocate<WriteTimestampCmd>(Command::WriteTimestamp);
             cmd->querySet = querySet;
diff --git a/src/dawn_native/CommandEncoder.h b/src/dawn_native/CommandEncoder.h
index 2fe801042c..8b5ae1f959 100644
--- a/src/dawn_native/CommandEncoder.h
+++ b/src/dawn_native/CommandEncoder.h
@@ -22,12 +22,15 @@
 #include "dawn_native/ObjectBase.h"
 #include "dawn_native/PassResourceUsage.h"
 
+#include <map>
 #include <string>
 
 namespace dawn_native {
 
     struct BeginRenderPassCmd;
 
+    using UsedQueryMap = std::map<QuerySetBase*, std::vector<bool>>;
+
     class CommandEncoder final : public ObjectBase {
       public:
         CommandEncoder(DeviceBase* device, const CommandEncoderDescriptor* descriptor);
@@ -36,6 +39,8 @@ namespace dawn_native {
         CommandBufferResourceUsage AcquireResourceUsages();
 
         void TrackUsedQuerySet(QuerySetBase* querySet);
+        void TrackUsedQueryIndex(QuerySetBase* querySet, uint32_t queryIndex);
+        const UsedQueryMap& GetUsedQueryIndices() const;
 
         // Dawn API
         ComputePassEncoder* BeginComputePass(const ComputePassDescriptor* descriptor);
@@ -77,6 +82,7 @@ namespace dawn_native {
         std::set<BufferBase*> mTopLevelBuffers;
         std::set<TextureBase*> mTopLevelTextures;
         std::set<QuerySetBase*> mUsedQuerySets;
+        UsedQueryMap mUsedQueryIndices;
     };
 
 }  // namespace dawn_native
diff --git a/src/dawn_native/CommandValidation.cpp b/src/dawn_native/CommandValidation.cpp
index 348d445f79..5e98cef65b 100644
--- a/src/dawn_native/CommandValidation.cpp
+++ b/src/dawn_native/CommandValidation.cpp
@@ -351,7 +351,9 @@ namespace dawn_native {
         return {};
     }
 
-    MaybeError ValidateTimestampQuery(QuerySetBase* querySet, uint32_t queryIndex) {
+    MaybeError ValidateTimestampQuery(QuerySetBase* querySet,
+                                      uint32_t queryIndex,
+                                      const UsedQueryMap& usedQueryIndices) {
         if (querySet->GetQueryType() != wgpu::QueryType::Timestamp) {
             return DAWN_VALIDATION_ERROR("The query type of query set must be Timestamp");
         }
@@ -360,6 +362,15 @@ namespace dawn_native {
             return DAWN_VALIDATION_ERROR("Query index exceeds the number of queries in query set");
         }
 
+        UsedQueryMap::const_iterator it = usedQueryIndices.find(querySet);
+        if (it != usedQueryIndices.end()) {
+            // Get the used query index records
+            const std::vector<bool>& queryIndices = it->second;
+            if (queryIndices[queryIndex] == 1) {
+                return DAWN_VALIDATION_ERROR("Duplicated query index writen");
+            }
+        }
+
         return {};
     }
 
diff --git a/src/dawn_native/CommandValidation.h b/src/dawn_native/CommandValidation.h
index eed2e6fae2..77714f4cc5 100644
--- a/src/dawn_native/CommandValidation.h
+++ b/src/dawn_native/CommandValidation.h
@@ -19,6 +19,7 @@
 #include "dawn_native/Error.h"
 #include "dawn_native/Texture.h"
 
+#include <map>
 #include <vector>
 
 namespace dawn_native {
@@ -29,6 +30,8 @@ namespace dawn_native {
     struct PassResourceUsage;
     struct TexelBlockInfo;
 
+    using UsedQueryMap = std::map<QuerySetBase*, std::vector<bool>>;
+
     MaybeError ValidateCanPopDebugGroup(uint64_t debugGroupStackSize);
     MaybeError ValidateFinalDebugGroupStackSize(uint64_t debugGroupStackSize);
 
@@ -39,7 +42,9 @@ namespace dawn_native {
 
     MaybeError ValidatePassResourceUsage(const PassResourceUsage& usage);
 
-    MaybeError ValidateTimestampQuery(QuerySetBase* querySet, uint32_t queryIndex);
+    MaybeError ValidateTimestampQuery(QuerySetBase* querySet,
+                                      uint32_t queryIndex,
+                                      const UsedQueryMap& usedQueryIndices);
 
     ResultOrError<uint64_t> ComputeRequiredBytesInCopy(const TexelBlockInfo& blockInfo,
                                                        const Extent3D& copySize,
diff --git a/src/dawn_native/ComputePassEncoder.cpp b/src/dawn_native/ComputePassEncoder.cpp
index 8d070eab27..bfb0e7eac9 100644
--- a/src/dawn_native/ComputePassEncoder.cpp
+++ b/src/dawn_native/ComputePassEncoder.cpp
@@ -106,10 +106,13 @@ namespace dawn_native {
         mEncodingContext->TryEncode(this, [&](CommandAllocator* allocator) -> MaybeError {
             if (GetDevice()->IsValidationEnabled()) {
                 DAWN_TRY(GetDevice()->ValidateObject(querySet));
-                DAWN_TRY(ValidateTimestampQuery(querySet, queryIndex));
+                DAWN_TRY(ValidateTimestampQuery(querySet, queryIndex,
+                                                mCommandEncoder->GetUsedQueryIndices()));
                 mCommandEncoder->TrackUsedQuerySet(querySet);
             }
 
+            mCommandEncoder->TrackUsedQueryIndex(querySet, queryIndex);
+
             WriteTimestampCmd* cmd =
                 allocator->Allocate<WriteTimestampCmd>(Command::WriteTimestamp);
             cmd->querySet = querySet;
diff --git a/src/dawn_native/RenderPassEncoder.cpp b/src/dawn_native/RenderPassEncoder.cpp
index 4d25107d94..df995633c2 100644
--- a/src/dawn_native/RenderPassEncoder.cpp
+++ b/src/dawn_native/RenderPassEncoder.cpp
@@ -180,10 +180,13 @@ namespace dawn_native {
         mEncodingContext->TryEncode(this, [&](CommandAllocator* allocator) -> MaybeError {
             if (GetDevice()->IsValidationEnabled()) {
                 DAWN_TRY(GetDevice()->ValidateObject(querySet));
-                DAWN_TRY(ValidateTimestampQuery(querySet, queryIndex));
+                DAWN_TRY(ValidateTimestampQuery(querySet, queryIndex,
+                                                mCommandEncoder->GetUsedQueryIndices()));
                 mCommandEncoder->TrackUsedQuerySet(querySet);
             }
 
+            mCommandEncoder->TrackUsedQueryIndex(querySet, queryIndex);
+
             WriteTimestampCmd* cmd =
                 allocator->Allocate<WriteTimestampCmd>(Command::WriteTimestamp);
             cmd->querySet = querySet;
diff --git a/src/tests/unittests/validation/QuerySetValidationTests.cpp b/src/tests/unittests/validation/QuerySetValidationTests.cpp
index 5bf7babdd3..ef53bd30ee 100644
--- a/src/tests/unittests/validation/QuerySetValidationTests.cpp
+++ b/src/tests/unittests/validation/QuerySetValidationTests.cpp
@@ -185,6 +185,14 @@ TEST_F(TimestampQueryValidationTest, WriteTimestampOnCommandEncoder) {
         ASSERT_DEVICE_ERROR(encoder.Finish());
     }
 
+    // Fail to write timestamp to the same index twice on command encoder
+    {
+        wgpu::CommandEncoder encoder = deviceWithTimestamp.CreateCommandEncoder();
+        encoder.WriteTimestamp(timestampQuerySet, 0);
+        encoder.WriteTimestamp(timestampQuerySet, 0);
+        ASSERT_DEVICE_ERROR(encoder.Finish());
+    }
+
     // Fail to submit timestamp query with a destroyed query set
     {
         wgpu::CommandEncoder encoder = deviceWithTimestamp.CreateCommandEncoder();
@@ -241,6 +249,26 @@ TEST_F(TimestampQueryValidationTest, WriteTimestampOnComputePassEncoder) {
         ASSERT_DEVICE_ERROR(encoder.Finish());
     }
 
+    // Fail to write timestamp to the same index twice on compute encoder
+    {
+        wgpu::CommandEncoder encoder = deviceWithTimestamp.CreateCommandEncoder();
+        wgpu::ComputePassEncoder pass = encoder.BeginComputePass();
+        pass.WriteTimestamp(timestampQuerySet, 0);
+        pass.WriteTimestamp(timestampQuerySet, 0);
+        pass.EndPass();
+        ASSERT_DEVICE_ERROR(encoder.Finish());
+    }
+
+    // Fail to write timestamp to the same index twice on command encoder and compute encoder
+    {
+        wgpu::CommandEncoder encoder = deviceWithTimestamp.CreateCommandEncoder();
+        encoder.WriteTimestamp(timestampQuerySet, 0);
+        wgpu::ComputePassEncoder pass = encoder.BeginComputePass();
+        pass.WriteTimestamp(timestampQuerySet, 0);
+        pass.EndPass();
+        ASSERT_DEVICE_ERROR(encoder.Finish());
+    }
+
     // Fail to submit timestamp query with a destroyed query set
     {
         wgpu::CommandEncoder encoder = deviceWithTimestamp.CreateCommandEncoder();
@@ -301,6 +329,26 @@ TEST_F(TimestampQueryValidationTest, WriteTimestampOnRenderPassEncoder) {
         ASSERT_DEVICE_ERROR(encoder.Finish());
     }
 
+    // Fail to write timestamp to the same index twice on command encoder and render encoder
+    {
+        wgpu::CommandEncoder encoder = deviceWithTimestamp.CreateCommandEncoder();
+        wgpu::RenderPassEncoder pass = encoder.BeginRenderPass(&renderPass);
+        pass.WriteTimestamp(timestampQuerySet, 0);
+        pass.WriteTimestamp(timestampQuerySet, 0);
+        pass.EndPass();
+        ASSERT_DEVICE_ERROR(encoder.Finish());
+    }
+
+    // Fail to write timestamp to the same index twice on command encoder and render encoder
+    {
+        wgpu::CommandEncoder encoder = deviceWithTimestamp.CreateCommandEncoder();
+        encoder.WriteTimestamp(timestampQuerySet, 0);
+        wgpu::RenderPassEncoder pass = encoder.BeginRenderPass(&renderPass);
+        pass.WriteTimestamp(timestampQuerySet, 0);
+        pass.EndPass();
+        ASSERT_DEVICE_ERROR(encoder.Finish());
+    }
+
     // Fail to submit timestamp query with a destroyed query set
     {
         wgpu::CommandEncoder encoder = deviceWithTimestamp.CreateCommandEncoder();