diff --git a/spacy/tests/doc/test_retokenize_merge.py b/spacy/tests/doc/test_retokenize_merge.py
index 28f00aa18..5bdf78f39 100644
--- a/spacy/tests/doc/test_retokenize_merge.py
+++ b/spacy/tests/doc/test_retokenize_merge.py
@@ -414,3 +414,14 @@ def test_doc_retokenizer_merge_lex_attrs(en_vocab):
     assert doc[1].is_stop
     assert not doc[0].is_stop
     assert not doc[1].like_num
+
+
+def test_retokenize_skip_duplicates(en_vocab):
+    """Test that the retokenizer automatically skips duplicate spans instead
+    of complaining about overlaps. See #3687."""
+    doc = Doc(en_vocab, words=["hello", "world", "!"])
+    with doc.retokenize() as retokenizer:
+        retokenizer.merge(doc[0:2])
+        retokenizer.merge(doc[0:2])
+    assert len(doc) == 2
+    assert doc[0].text == "hello world"
diff --git a/spacy/tokens/_retokenize.pyx b/spacy/tokens/_retokenize.pyx
index 5b0747fa0..f8b13dd78 100644
--- a/spacy/tokens/_retokenize.pyx
+++ b/spacy/tokens/_retokenize.pyx
@@ -35,12 +35,14 @@ cdef class Retokenizer:
     cdef list merges
     cdef list splits
     cdef set tokens_to_merge
+    cdef list _spans_to_merge
 
     def __init__(self, doc):
         self.doc = doc
         self.merges = []
         self.splits = []
         self.tokens_to_merge = set()
+        self._spans_to_merge = []  # keep a record to filter out duplicates
 
     def merge(self, Span span, attrs=SimpleFrozenDict()):
         """Mark a span for merging. The attrs will be applied to the resulting
@@ -51,10 +53,13 @@ cdef class Retokenizer:
 
         DOCS: https://spacy.io/api/doc#retokenizer.merge
         """
+        if (span.start, span.end) in self._spans_to_merge:
+            return
         for token in span:
             if token.i in self.tokens_to_merge:
                 raise ValueError(Errors.E102.format(token=repr(token)))
             self.tokens_to_merge.add(token.i)
+        self._spans_to_merge.append((span.start, span.end))
         if "_" in attrs:  # Extension attributes
             extensions = attrs["_"]
             _validate_extensions(extensions)