diff --git a/test/blackbox-tests/test-cases/merlin/include-subdirs-qualified.t b/test/blackbox-tests/test-cases/merlin/include-subdirs-qualified.t
new file mode 100644
index 00000000000..26d7b8d2074
--- /dev/null
+++ b/test/blackbox-tests/test-cases/merlin/include-subdirs-qualified.t
@@ -0,0 +1,161 @@
+  $ cat >dune-project <<EOF
+  > (lang dune 3.12)
+  > EOF
+
+  $ cat >dune <<EOF
+  > (include_subdirs qualified)
+  > (library
+  >  (name foo))
+  > EOF
+
+  $ touch main.ml
+  $ mkdir utils
+  $ touch utils/calc.ml
+
+  $ mkdir groupintf
+  $ touch groupintf/groupintf.ml
+  $ touch groupintf/calc.ml
+
+  $ opam_prefix="$(ocamlc -where)"
+  $ export BUILD_PATH_PREFIX_MAP="/OPAM_PREFIX=$opam_prefix:$BUILD_PATH_PREFIX_MAP"
+
+  $ dune build .merlin-conf/lib-foo
+  $ dune ocaml merlin dump-config .
+  Foo: _build/default/foo
+  ((STDLIB /OPAM_PREFIX)
+   (EXCLUDE_QUERY_DIR)
+   (B
+    $TESTCASE_ROOT/_build/default/.foo.objs/byte)
+   (S
+    $TESTCASE_ROOT)
+   (S
+    $TESTCASE_ROOT/groupintf)
+   (S
+    $TESTCASE_ROOT/utils)
+   (FLG
+    (-w
+     @1..3@5..28@30..39@43@46..47@49..57@61..62@67@69-40
+     -strict-sequence
+     -strict-formats
+     -short-paths
+     -keep-locs
+     -g)))
+  Foo__Groupintf__: _build/default/foo__Groupintf__
+  ((STDLIB /OPAM_PREFIX)
+   (EXCLUDE_QUERY_DIR)
+   (B
+    $TESTCASE_ROOT/_build/default/.foo.objs/byte)
+   (S
+    $TESTCASE_ROOT)
+   (S
+    $TESTCASE_ROOT/groupintf)
+   (S
+    $TESTCASE_ROOT/utils)
+   (FLG
+    (-w
+     @1..3@5..28@30..39@43@46..47@49..57@61..62@67@69-40
+     -strict-sequence
+     -strict-formats
+     -short-paths
+     -keep-locs
+     -g)))
+  Utils: _build/default/foo__Utils
+  ((STDLIB /OPAM_PREFIX)
+   (EXCLUDE_QUERY_DIR)
+   (B
+    $TESTCASE_ROOT/_build/default/.foo.objs/byte)
+   (S
+    $TESTCASE_ROOT)
+   (S
+    $TESTCASE_ROOT/groupintf)
+   (S
+    $TESTCASE_ROOT/utils)
+   (FLG
+    (-w
+     @1..3@5..28@30..39@43@46..47@49..57@61..62@67@69-40
+     -strict-sequence
+     -strict-formats
+     -short-paths
+     -keep-locs
+     -g)))
+  Calc: _build/default/groupintf/calc
+  ((STDLIB /OPAM_PREFIX)
+   (EXCLUDE_QUERY_DIR)
+   (B
+    $TESTCASE_ROOT/_build/default/.foo.objs/byte)
+   (S
+    $TESTCASE_ROOT)
+   (S
+    $TESTCASE_ROOT/groupintf)
+   (S
+    $TESTCASE_ROOT/utils)
+   (FLG (-open Foo__Groupintf__ -open Foo))
+   (FLG
+    (-w
+     @1..3@5..28@30..39@43@46..47@49..57@61..62@67@69-40
+     -strict-sequence
+     -strict-formats
+     -short-paths
+     -keep-locs
+     -g)))
+  Groupintf: _build/default/groupintf/groupintf
+  ((STDLIB /OPAM_PREFIX)
+   (EXCLUDE_QUERY_DIR)
+   (B
+    $TESTCASE_ROOT/_build/default/.foo.objs/byte)
+   (S
+    $TESTCASE_ROOT)
+   (S
+    $TESTCASE_ROOT/groupintf)
+   (S
+    $TESTCASE_ROOT/utils)
+   (FLG (-open Foo__Groupintf__ -open Foo))
+   (FLG
+    (-w
+     @1..3@5..28@30..39@43@46..47@49..57@61..62@67@69-40
+     -strict-sequence
+     -strict-formats
+     -short-paths
+     -keep-locs
+     -g)))
+  Main: _build/default/main
+  ((STDLIB /OPAM_PREFIX)
+   (EXCLUDE_QUERY_DIR)
+   (B
+    $TESTCASE_ROOT/_build/default/.foo.objs/byte)
+   (S
+    $TESTCASE_ROOT)
+   (S
+    $TESTCASE_ROOT/groupintf)
+   (S
+    $TESTCASE_ROOT/utils)
+   (FLG (-open Foo))
+   (FLG
+    (-w
+     @1..3@5..28@30..39@43@46..47@49..57@61..62@67@69-40
+     -strict-sequence
+     -strict-formats
+     -short-paths
+     -keep-locs
+     -g)))
+  Calc: _build/default/utils/calc
+  ((STDLIB /OPAM_PREFIX)
+   (EXCLUDE_QUERY_DIR)
+   (B
+    $TESTCASE_ROOT/_build/default/.foo.objs/byte)
+   (S
+    $TESTCASE_ROOT)
+   (S
+    $TESTCASE_ROOT/groupintf)
+   (S
+    $TESTCASE_ROOT/utils)
+   (FLG (-open Utils -open Foo))
+   (FLG
+    (-w
+     @1..3@5..28@30..39@43@46..47@49..57@61..62@67@69-40
+     -strict-sequence
+     -strict-formats
+     -short-paths
+     -keep-locs
+     -g)))
+  $ dune ocaml merlin dump-config utils