diff --git a/.circleci/config.yml b/.circleci/config.yml
index a5d250f2fb..7df5832ee2 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -116,14 +116,17 @@ jobs:
             ninja -C build-clang test
 
       - run:
-          name: Install shared library
+          name: Test building with meson subproject
           command: |
-            meson build-install c --prefix=/usr
-            sudo ninja -C build-install install
+            meson build-subproject c/tests/meson-subproject
+            ninja -C build-subproject
+            ./build-subproject/example
 
       - run:
-          name: Hand-compile some example programs
+          name: Install shared library and hand-compile program.
           command: |
+            meson build-install c --prefix=/usr
+            sudo ninja -C build-install install
             clang c/examples/api_structure.c -o api_structure -ltskit
             ./api_structure
 
diff --git a/.gitmodules b/.gitmodules
index d5a2923ff5..08c84692c3 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,3 +1,3 @@
 [submodule "c/kastore"]
-	path = c/kastore
+	path = c/subprojects/full-projects/kastore
 	url = https://github.com/tskit-dev/kastore.git
diff --git a/c/kastore b/c/kastore
deleted file mode 160000
index fb5933b64b..0000000000
--- a/c/kastore
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit fb5933b64b669b8126c4ac614788661dd0c248d2
diff --git a/c/meson.build b/c/meson.build
index 90276bef6b..ebef478e08 100644
--- a/c/meson.build
+++ b/c/meson.build
@@ -1,11 +1,11 @@
 project('tskit', ['c', 'cpp'], default_options: ['c_std=c99', 'cpp_std=c++11'])
 
-kastore_dir=join_paths(meson.source_root(), 'kastore/c')
-add_global_arguments(['-I' + kastore_dir], language: ['c', 'cpp'])
+kastore_proj = subproject('kastore')
+kastore_dep = kastore_proj.get_variable('kastore_dep')
 
 cc = meson.get_compiler('c')
 m_dep = cc.find_library('m', required: false)
-lib_deps = [m_dep]
+lib_deps = [m_dep, kastore_dep]
 
 extra_c_args = [
     '-Wall', '-Wextra', '-Werror', '-Wpedantic', '-W',
@@ -15,85 +15,85 @@ extra_c_args = [
     '-fshort-enums', '-fno-common']
 
 lib_sources = [
-    'kastore/c/kastore.c', 'tskit/core.c', 'tskit/tables.c', 'tskit/trees.c', 
+    'tskit/core.c', 'tskit/tables.c', 'tskit/trees.c', 
     'tskit/genotypes.c', 'tskit/stats.c', 'tskit/convert.c']
 lib_headers = [
     'tskit/core.h', 'tskit/tables.h', 'tskit/trees.h', 
     'tskit/genotypes.h', 'tskit/stats.h', 'tskit/convert.h']
 
+# Subprojects use the static library for simplicity.
+inc = include_directories(['.', 'tskit'])
+tskit_lib = static_library('tskit', 
+    sources: lib_sources, dependencies: lib_deps)
+tskit_dep = declare_dependency(include_directories:inc, link_with: tskit_lib)
 
-# Shared library install target.
-shared_library('tskit', 
-    sources: lib_sources, dependencies: lib_deps, c_args: extra_c_args, install: true)
-# FIXME for now we include the kastore header because the shared lib won't 
-# work otherwise. Will need to come up with a better solution for this.
-install_headers('kastore/c/kastore.h')
-install_headers('tskit.h')
-install_headers(lib_headers, subdir: 'tskit') 
+if not meson.is_subproject()
 
-# Static library for building tests and examples.
-tskit_lib = static_library('tskit', 
-    sources: lib_sources, dependencies: lib_deps, c_args: extra_c_args)
+    # Shared library install target.
+    shared_library('tskit', 
+        sources: lib_sources, dependencies: lib_deps, c_args: extra_c_args, install: true)
+    install_headers('tskit.h')
+    install_headers(lib_headers, subdir: 'tskit') 
 
-cunit_dep = dependency('cunit', required: false)
-if cunit_dep.found()
+    cunit_dep = dependency('cunit')
     # We don't specify extra C args here as CUnit won't pass the checks.
     test_lib = static_library('testlib', 
-        sources: ['tests/testlib.c'], dependencies: cunit_dep)
+        sources: ['tests/testlib.c'], dependencies: [cunit_dep, kastore_dep])
 
     test_core = executable('test_core', 
         sources: ['tests/test_core.c'], 
-        link_with: [tskit_lib, test_lib], c_args: extra_c_args)
+        link_with: [tskit_lib, test_lib], c_args: extra_c_args, dependencies: kastore_dep)
     test('core', test_core)
 
     test_tables = executable('test_tables', 
         sources: ['tests/test_tables.c'], 
-        link_with: [tskit_lib, test_lib], c_args: extra_c_args)
+        link_with: [tskit_lib, test_lib], c_args: extra_c_args, dependencies: kastore_dep)
     test('tables', test_tables)
 
     test_trees = executable('test_trees', 
         sources: ['tests/test_trees.c'], 
-        link_with: [tskit_lib, test_lib], c_args: extra_c_args)
+        link_with: [tskit_lib, test_lib], c_args: extra_c_args, dependencies: kastore_dep)
     test('trees', test_trees)
 
     test_genotypes = executable('test_genotypes', 
         sources: ['tests/test_genotypes.c'], 
-        link_with: [tskit_lib, test_lib], c_args: extra_c_args)
+        link_with: [tskit_lib, test_lib], c_args: extra_c_args, dependencies: kastore_dep)
     test('genotypes', test_genotypes)
 
     test_convert = executable('test_convert', 
         sources: ['tests/test_convert.c'], 
-        link_with: [tskit_lib, test_lib], c_args: extra_c_args)
+        link_with: [tskit_lib, test_lib], c_args: extra_c_args, dependencies: kastore_dep)
     test('convert', test_convert)
          
     test_stats = executable('test_stats', 
         sources: ['tests/test_stats.c'], 
-        link_with: [tskit_lib, test_lib], c_args: extra_c_args)
+        link_with: [tskit_lib, test_lib], c_args: extra_c_args, dependencies: kastore_dep)
     test('stats', test_stats)
-endif
 
-test_minimal_cpp = executable('test_minimal_cpp', 
-    sources: ['tests/test_minimal_cpp.cpp'], link_with: [tskit_lib])
-test('minimal_cpp', test_minimal_cpp)
-
-# The development CLI. Don't use extra C args because argtable code won't pass
-executable('dev-cli', 
-    sources: ['dev-tools/dev-cli.c', 'dev-tools/argtable3.c'], 
-    link_with: [tskit_lib], c_args:['-Dlint'])
-
-# Example programs. 
-executable('api_structure', 
-    sources: ['examples/api_structure.c'], link_with: [tskit_lib])
-executable('error_handling', 
-    sources: ['examples/error_handling.c'], link_with: [tskit_lib])
-executable('tree_iteration', 
-    sources: ['examples/tree_iteration.c'], link_with: [tskit_lib])
-
-gsl_dep = dependency('gsl', required: false)
-if gsl_dep.found()
-    executable('haploid_wright_fisher', 
-        sources: ['examples/haploid_wright_fisher.c'], link_with: [tskit_lib],
-        dependencies: [gsl_dep])
+    test_minimal_cpp = executable('test_minimal_cpp', 
+        sources: ['tests/test_minimal_cpp.cpp'], link_with: [tskit_lib],
+        dependencies: kastore_dep)
+    test('minimal_cpp', test_minimal_cpp)
+
+    # The development CLI. Don't use extra C args because argtable code won't pass
+    executable('dev-cli', 
+        sources: ['dev-tools/dev-cli.c', 'dev-tools/argtable3.c'], 
+        link_with: [tskit_lib], c_args:['-Dlint'], dependencies: kastore_dep)
+
+    # Example programs. 
+    executable('api_structure', 
+        sources: ['examples/api_structure.c'], link_with: [tskit_lib], dependencies: lib_deps)
+    executable('error_handling', 
+        sources: ['examples/error_handling.c'], link_with: [tskit_lib], dependencies: lib_deps)
+    executable('tree_iteration', 
+        sources: ['examples/tree_iteration.c'], link_with: [tskit_lib], dependencies: lib_deps)
+
+    gsl_dep = dependency('gsl', required: false)
+    if gsl_dep.found()
+        executable('haploid_wright_fisher', 
+            sources: ['examples/haploid_wright_fisher.c'], link_with: [tskit_lib],
+            dependencies: [gsl_dep, lib_deps])
+    endif
 endif
 
 # TMP: until we've ported all the tests, keep this compilable.
diff --git a/c/subprojects/full-projects/kastore b/c/subprojects/full-projects/kastore
new file mode 160000
index 0000000000..b15f21c0c0
--- /dev/null
+++ b/c/subprojects/full-projects/kastore
@@ -0,0 +1 @@
+Subproject commit b15f21c0c0d0a12800836154af4180e94a0714b5
diff --git a/c/subprojects/kastore b/c/subprojects/kastore
new file mode 120000
index 0000000000..ee3ac9b241
--- /dev/null
+++ b/c/subprojects/kastore
@@ -0,0 +1 @@
+full-projects/kastore/c/
\ No newline at end of file
diff --git a/c/tests/meson-subproject/example.c b/c/tests/meson-subproject/example.c
new file mode 100644
index 0000000000..05b2d81c73
--- /dev/null
+++ b/c/tests/meson-subproject/example.c
@@ -0,0 +1,59 @@
+/* Simple example testing that we compile and link in tskit and kastore
+ * when we use meson submodules.
+ */
+#include <stdio.h>
+#include <tskit.h>
+#include <assert.h>
+#include <string.h>
+
+void
+test_kas_strerror()
+{
+    printf("test_kas_strerror\n");
+    const char *str = kas_strerror(KAS_ERR_NO_MEMORY);
+    assert(strcmp(str, "Out of memory") == 0);
+}
+
+void
+test_strerror()
+{
+    printf("test_strerror\n");
+    const char *str = tsk_strerror(TSK_ERR_NO_MEMORY);
+    assert(strcmp(str, "Out of memory") == 0);
+}
+
+void
+test_load_error()
+{
+    printf("test_open_error\n");
+    tsk_treeseq_t ts;
+    int ret = tsk_treeseq_load(&ts, "no such file", 0);
+    assert(tsk_is_kas_error(ret));
+    tsk_treeseq_free(&ts);
+}
+
+void
+test_table_basics()
+{
+    printf("test_table_basics\n");
+    tsk_table_collection_t tables;
+    int ret = tsk_table_collection_init(&tables, 0);
+    assert(ret == 0);
+
+    ret = tsk_node_table_add_row(&tables.nodes, 0, 1.0, TSK_NULL, TSK_NULL, NULL, 0);
+    assert(ret == 0);
+    ret = tsk_node_table_add_row(&tables.nodes, 0, 2.0, TSK_NULL, TSK_NULL, NULL, 0);
+    assert(ret == 1);
+    assert(tables.nodes.num_rows == 2);
+
+    tsk_table_collection_free(&tables);
+}
+
+int main()
+{
+    test_kas_strerror();
+    test_strerror();
+    test_load_error();
+    test_table_basics();
+    return 0;
+}
diff --git a/c/tests/meson-subproject/meson.build b/c/tests/meson-subproject/meson.build
new file mode 100644
index 0000000000..ee4218db18
--- /dev/null
+++ b/c/tests/meson-subproject/meson.build
@@ -0,0 +1,12 @@
+project('example', 'c')
+
+kastore_proj = subproject('kastore')
+kastore_dep = kastore_proj.get_variable('kastore_dep')
+tskit_proj = subproject('tskit')
+tskit_dep = tskit_proj.get_variable('tskit_dep')
+
+executable('example',
+  'example.c',
+   dependencies : [kastore_dep, tskit_dep],
+   install : true)
+
diff --git a/c/tests/meson-subproject/subprojects/kastore b/c/tests/meson-subproject/subprojects/kastore
new file mode 120000
index 0000000000..ff09d40cad
--- /dev/null
+++ b/c/tests/meson-subproject/subprojects/kastore
@@ -0,0 +1 @@
+../../../subprojects/full-projects/kastore/c/
\ No newline at end of file
diff --git a/c/tests/meson-subproject/subprojects/tskit b/c/tests/meson-subproject/subprojects/tskit
new file mode 120000
index 0000000000..1b20c9fb81
--- /dev/null
+++ b/c/tests/meson-subproject/subprojects/tskit
@@ -0,0 +1 @@
+../../../
\ No newline at end of file
diff --git a/python/MANIFEST.in b/python/MANIFEST.in
index b918a4ab8d..efefe9f1fe 100644
--- a/python/MANIFEST.in
+++ b/python/MANIFEST.in
@@ -1,4 +1,4 @@
-include lib/kastore/c/kastore.h
+include lib/subprojects/kastore/kastore.h
 include lib/tskit.h
 include lib/tskit/*.h
 include LICENSE
diff --git a/python/setup.py b/python/setup.py
index 59878144c6..9db138ff71 100644
--- a/python/setup.py
+++ b/python/setup.py
@@ -25,7 +25,7 @@ def finalize_options(self):
 
 
 libdir = "lib"
-kastore_dir = os.path.join(libdir, "kastore", "c")
+kastore_dir = os.path.join(libdir, "subprojects", "kastore")
 tsk_source_files = [
     "core.c",
     "tables.c",