diff --git a/pkgs/applications/science/biology/bowtie/default.nix b/pkgs/applications/science/biology/bowtie/default.nix
index 81cdaecf2c1..ccb797d8a22 100644
--- a/pkgs/applications/science/biology/bowtie/default.nix
+++ b/pkgs/applications/science/biology/bowtie/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchFromGitHub, zlib }:
+{ lib, stdenv, fetchFromGitHub, fetchpatch, zlib }:
 
 stdenv.mkDerivation rec {
   pname = "bowtie";
@@ -11,6 +11,26 @@ stdenv.mkDerivation rec {
     sha256 = "sha256-mWItmrTMPst/NnzSpxxTHcBztDqHPCza9yOsZPwp7G4=";
   };
 
+  patches = [
+    # Without this patch, compiling with clang on an M1 Mac fails because
+    # 'cpuid.h' is included. It only works on x86 and throws an error.
+    (fetchpatch {
+      name = "fix_compilation_on_arm64";
+      url = "https://github.com/BenLangmead/bowtie/commit/091d72f4cb69ca0713704d38bd7f9b37e6c4ff2d.patch";
+      sha256 = "sha256-XBvgICUBnE5HKpJ36IHTDiKjJgLFKETsIaJC46uN+2I=";
+    })
+
+    # Without this patch, compilation adds the current source directory to the
+    # include search path, and #include <version> in standard library code can
+    # end up picking the unrelated VERSION source code file on case-insensitive
+    # file systems.
+    (fetchpatch {
+      name = "fix_include_search_path";
+      url = "https://github.com/BenLangmead/bowtie/commit/c208b9db936eab0bc3ffdf0182b4f59a9017a1c4.patch";
+      sha256 = "sha256-772EE+oWFWXssSMabPryb0AfIS1tC10mPTRCBm7RrUs=";
+    })
+  ];
+
   buildInputs = [ zlib ];
 
   installFlags = [ "prefix=$(out)" ];