diff --git a/pkgs/applications/science/biology/obitools/obitools3.nix b/pkgs/applications/science/biology/obitools/obitools3.nix
new file mode 100644
index 000000000000..076e459c8f0b
--- /dev/null
+++ b/pkgs/applications/science/biology/obitools/obitools3.nix
@@ -0,0 +1,38 @@
+{ stdenv, fetchurl, python3Packages, cmake, python3 }:
+
+let
+  pythonPackages = python3Packages;
+in
+
+pythonPackages.buildPythonApplication rec {
+  pname = "obitools3";
+  version = "3.0.0-beta14";
+
+  src = fetchurl {
+    url = "https://git.metabarcoding.org/obitools/${pname}/repository/v${version}/archive.tar.gz";
+    sha256 = "17krklxfvxl6baf2m394gm1a88y0lg0bwqx20cf5q39zyw04z442";
+  };
+
+  preBuild = ''
+    substituteInPlace src/CMakeLists.txt --replace \$'{PYTHONLIB}' "$out/lib/${python3.libPrefix}/site-packages";
+    export NIX_CFLAGS_COMPILE="-L $out/lib/${python3.libPrefix}/site-packages $NIX_CFLAGS_COMPILE"
+  '';
+
+  disabled = !pythonPackages.isPy3k;
+
+  nativeBuildInputs = [ pythonPackages.cython cmake ];
+
+  dontConfigure = true;
+
+  doCheck = true;
+
+  enableParallelBuilding = true;
+
+  meta = with stdenv.lib ; {
+    description = "Management of analyses and data in DNA metabarcoding";
+    homepage = "https://git.metabarcoding.org/obitools/obitools3";
+    license = licenses.cecill20;
+    maintainers = [ maintainers.bzizou ];
+    platforms = platforms.all;
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 209bf1848453..4f2177d41e07 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -24435,6 +24435,8 @@ in
 
   manta = callPackage ../applications/science/biology/manta { };
 
+  obitools3 = callPackage ../applications/science/biology/obitools/obitools3.nix { };
+
   octopus-caller = callPackage ../applications/science/biology/octopus { };
 
   paml = callPackage ../applications/science/biology/paml { };