diff --git a/git-submodules/tskit b/git-submodules/tskit
index 76b658163..d3f7642af 160000
--- a/git-submodules/tskit
+++ b/git-submodules/tskit
@@ -1 +1 @@
-Subproject commit 76b658163101c2d4c82843665e521e139b74d738
+Subproject commit d3f7642aff221dff16cfe4cf261bca820b22d014
diff --git a/lib/subprojects/tskit.wrap b/lib/subprojects/tskit.wrap
index 777b1874a..7782d5745 100644
--- a/lib/subprojects/tskit.wrap
+++ b/lib/subprojects/tskit.wrap
@@ -1,6 +1,6 @@
 [wrap-file]
-directory = tskit-1.0.0
+directory = tskit-1.2.0
 
-source_url = https://github.com/tskit-dev/tskit/releases/download/C_1.0.0/tskit-1.0.0.tar.xz
-source_filename = tskit-1.0.0.tar.xz
-source_hash = f8a085fc6ef170706b76a307e18be4ab425f31a1f50fa9765ab2c2d81eef65c2
+source_url = https://github.com/tskit-dev/tskit/releases/download/C_1.2.0/tskit-1.2.0.tar.xz
+source_filename = tskit-1.2.0.tar.xz
+source_hash = f8f4c341b34df3620404ba8d6c362e3bb7257d48962373c6499871fc2e26b388
diff --git a/lib/tests/test_core.c b/lib/tests/test_core.c
index 06239bf66..9cc30d22b 100644
--- a/lib/tests/test_core.c
+++ b/lib/tests/test_core.c
@@ -126,7 +126,7 @@ test_tskit_version(void)
 {
     /* Make sure we don't have any accidental changes to the tskit submodule. */
     CU_ASSERT_EQUAL(TSK_VERSION_MAJOR, 1);
-    CU_ASSERT_EQUAL(TSK_VERSION_MINOR, 0);
+    CU_ASSERT_EQUAL(TSK_VERSION_MINOR, 2);
     CU_ASSERT_EQUAL(TSK_VERSION_PATCH, 0);
 }
 
diff --git a/setup.py b/setup.py
index 7f144b9f6..9750b5ac2 100644
--- a/setup.py
+++ b/setup.py
@@ -82,7 +82,7 @@ def get_extension():
         "mutgen.c",
         "likelihood.c",
     ]
-    tsk_source_files = ["core.c", "tables.c", "trees.c"]
+    tsk_source_files = ["core.c", "tables.c", "trees.c", "genotypes.c"]
     kas_source_files = ["kastore.c"]
 
     sources = (
diff --git a/tests/test_lowlevel.py b/tests/test_lowlevel.py
index 73d2812e5..8a4f20cec 100644
--- a/tests/test_lowlevel.py
+++ b/tests/test_lowlevel.py
@@ -440,7 +440,7 @@ def test_gsl_error_handler(self):
     def test_tsk_library_version(self):
         tsk_version = _msprime.get_tskit_c_version()
         # Update this when the tskit C library version changes
-        assert tsk_version == (1, 0, 0)
+        assert tsk_version == (1, 2, 0)
 
 
 def get_random_population_models(n):