diff --git a/pkgs/top-level/aliases.nix b/pkgs/top-level/aliases.nix
index 83f14e5dd50..12d338b4c12 100644
--- a/pkgs/top-level/aliases.nix
+++ b/pkgs/top-level/aliases.nix
@@ -620,6 +620,7 @@ mapAliases ({
   phonon-backend-gstreamer = throw "phonon-backend-gstreamer: Please use libsForQt5.phonon-backend-gstreamer, as Qt4 support in this package has been removed."; # added 2019-11-22
   phonon-backend-vlc = throw "phonon-backend-vlc: Please use libsForQt5.phonon-backend-vlc, as Qt4 support in this package has been removed."; # added 2019-11-22
   phonon = throw "phonon: Please use libsForQt5.phonon, as Qt4 support in this package has been removed."; # added 2019-11-22
+  pybind11 = throw "pybind11 was removed because pythonPackages.pybind11 for the appropriate version of Python should be used"; # added 2021-05-14
   pynagsystemd = throw "pynagsystemd was removed as it was unmaintained and incompatible with recent systemd versions. Instead use its fork check_systemd."; # added 2020-10-24
   python2nix = throw "python2nix has been removed as it is outdated. Use e.g. nixpkgs-pytools instead."; # added 2021-03-08
   quagga = throw "quagga is no longer maintained upstream"; # added 2021-04-22
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 2d1f7af063d..c030fb9453f 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -17328,8 +17328,6 @@ in
 
   pugixml = callPackage ../development/libraries/pugixml { };
 
-  pybind11 = pythonPackages.pybind11;
-
   pylode = callPackage ../misc/pylode {};
 
   python-qt = callPackage ../development/libraries/python-qt {