diff --git a/docs/api.rst b/docs/api.rst
index 113a0658e..512a3ccda 100644
--- a/docs/api.rst
+++ b/docs/api.rst
@@ -23,6 +23,10 @@ BGEN
 PLINK
 -----
 
+.. deprecated:: 0.11.0
+   Functions for reading and writing plink are deprecated, please use the `bio2zarr <https://github.com/sgkit-dev/bio2zarr>`_
+   and `vcztools <https://github.com/sgkit-dev/vcztools>`_ packages.
+
 .. currentmodule:: sgkit.io.plink
 .. autosummary::
    :toctree: generated/
diff --git a/docs/changelog.rst b/docs/changelog.rst
index ec104cbbf..ea57b00ff 100644
--- a/docs/changelog.rst
+++ b/docs/changelog.rst
@@ -14,8 +14,12 @@ Changelog
 .. Breaking changes
 .. ~~~~~~~~~~~~~~~~
 
-.. Deprecations
-.. ~~~~~~~~~~~~
+Deprecations
+~~~~~~~~~~~~
+
+- Functions for reading and writing plink are deprecated, please use the `bio2zarr <https://github.com/sgkit-dev/bio2zarr>`_
+  and `vcztools <https://github.com/sgkit-dev/vcztools>`_ packages.
+  (:user:`tomwhite`, :pr:`1324`, :issue:`1318`)
 
 .. Improvements
 .. ~~~~~~~~~~~~
diff --git a/sgkit/io/plink/__init__.py b/sgkit/io/plink/__init__.py
index ea42b16ca..7e63c7ce1 100644
--- a/sgkit/io/plink/__init__.py
+++ b/sgkit/io/plink/__init__.py
@@ -1,3 +1,11 @@
+import warnings
+
+warnings.warn(
+    "Functions for reading and writing plink are deprecated, please use the bio2zarr and vcztools packages.",
+    DeprecationWarning,
+    stacklevel=2,
+)
+
 try:
     from .plink_reader import plink_to_zarr, read_plink
     from .plink_writer import write_plink, zarr_to_plink
diff --git a/sgkit/io/plink/plink_reader.py b/sgkit/io/plink/plink_reader.py
index 274d3208c..b6da1c012 100644
--- a/sgkit/io/plink/plink_reader.py
+++ b/sgkit/io/plink/plink_reader.py
@@ -147,6 +147,10 @@ def read_plink(
     Loads a single PLINK dataset as dask arrays within a Dataset
     from bed, bim, and fam files.
 
+    .. deprecated:: 0.11.0
+        Functions for reading and writing plink are deprecated, please use the `bio2zarr <https://github.com/sgkit-dev/bio2zarr>`_
+        and `vcztools <https://github.com/sgkit-dev/vcztools>`_ packages.
+
     Parameters
     ----------
     path
@@ -328,6 +332,10 @@ def plink_to_zarr(
 
     Refer to :func:`read_plink` for details and limitations.
 
+    .. deprecated:: 0.11.0
+        Functions for reading and writing plink are deprecated, please use the `bio2zarr <https://github.com/sgkit-dev/bio2zarr>`_
+        and `vcztools <https://github.com/sgkit-dev/vcztools>`_ packages.
+
     Parameters
     ----------
     path
diff --git a/sgkit/io/plink/plink_writer.py b/sgkit/io/plink/plink_writer.py
index 4b5bc9bed..42939b492 100644
--- a/sgkit/io/plink/plink_writer.py
+++ b/sgkit/io/plink/plink_writer.py
@@ -49,6 +49,10 @@ def write_plink(
     - ``sample_phenotype``: Phenotype code equal to 1 for control, 2 for case,
         and -1 for missing
 
+    .. deprecated:: 0.11.0
+        Functions for reading and writing plink are deprecated, please use the `bio2zarr <https://github.com/sgkit-dev/bio2zarr>`_
+        and `vcztools <https://github.com/sgkit-dev/vcztools>`_ packages.
+
     Parameters
     ----------
     ds
@@ -146,6 +150,10 @@ def zarr_to_plink(
 
     Refer to :func:`write_plink` for details and limitations.
 
+    .. deprecated:: 0.11.0
+        Functions for reading and writing plink are deprecated, please use the `bio2zarr <https://github.com/sgkit-dev/bio2zarr>`_
+        and `vcztools <https://github.com/sgkit-dev/vcztools>`_ packages.
+
     Parameters
     ----------
     input