diff --git a/piptools/sync.py b/piptools/sync.py
index 579436a34..430b4bb6f 100644
--- a/piptools/sync.py
+++ b/piptools/sync.py
@@ -82,18 +82,19 @@ def merge(requirements, ignore_conflicts):
         # Limitation: URL requirements are merged by precise string match, so
         # "file:///example.zip#egg=example", "file:///example.zip", and
         # "example==1.0" will not merge with each other
-        key = key_from_ireq(ireq)
-
-        if not ignore_conflicts:
-            existing_ireq = by_key.get(key)
-            if existing_ireq:
-                # NOTE: We check equality here since we can assume that the
-                # requirements are all pinned
-                if ireq.specifier != existing_ireq.specifier:
-                    raise IncompatibleRequirements(ireq, existing_ireq)
-
-        # TODO: Always pick the largest specifier in case of a conflict
-        by_key[key] = ireq
+        if ireq.match_markers():
+            key = key_from_ireq(ireq)
+
+            if not ignore_conflicts:
+                existing_ireq = by_key.get(key)
+                if existing_ireq:
+                    # NOTE: We check equality here since we can assume that the
+                    # requirements are all pinned
+                    if ireq.specifier != existing_ireq.specifier:
+                        raise IncompatibleRequirements(ireq, existing_ireq)
+
+            # TODO: Always pick the largest specifier in case of a conflict
+            by_key[key] = ireq
     return by_key.values()
 
 
diff --git a/tests/test_cli_sync.py b/tests/test_cli_sync.py
index ffc21720c..3f4de5cfa 100644
--- a/tests/test_cli_sync.py
+++ b/tests/test_cli_sync.py
@@ -93,21 +93,34 @@ def test_force_files_with_dot_in_extension(runner):
     assert out.exit_code == 0
 
 
-def test_merge_error(runner):
+@pytest.mark.parametrize(
+    ("req_lines", "should_raise"),
+    [
+        (["six>1.10.0", "six<1.10.0"], True),
+        (
+            ["six>1.10.0 ; python_version>='3.0'", "six<1.10.0 ; python_version<'3.0'"],
+            False,
+        ),
+    ],
+)
+def test_merge_error(req_lines, should_raise, runner):
     """
     Sync command should raise an error if there are merge errors.
+    It should not raise an error if otherwise incompatible requirements
+    are isolated by exclusive environment markers.
     """
     with open("requirements.txt", "w") as req_in:
-        req_in.write("six>1.10.0\n")
-
-        # Add incompatible package
-        req_in.write("six<1.10.0")
+        for line in req_lines:
+            req_in.write(line + "\n")
 
     with mock.patch("piptools.sync.check_call"):
         out = runner.invoke(cli, ["-n"])
 
-    assert out.exit_code == 2
-    assert "Incompatible requirements found" in out.stderr
+    if should_raise:
+        assert out.exit_code == 2
+        assert "Incompatible requirements found" in out.stderr
+    else:
+        assert out.exit_code == 0
 
 
 @pytest.mark.parametrize(