diff --git a/var/spack/repos/builtin/packages/tophat/package.py b/var/spack/repos/builtin/packages/tophat/package.py
index cd558eb76d8..b0d59bba3aa 100644
--- a/var/spack/repos/builtin/packages/tophat/package.py
+++ b/var/spack/repos/builtin/packages/tophat/package.py
@@ -29,6 +29,10 @@ class Tophat(AutotoolsPackage):
 
     parallel = False
 
+    def patch(self):
+        # Newer versions of autoconf hate calling AM_INIT_AUTOMAKE twice
+        filter_file(r"^AM_INIT_AUTOMAKE$", "", "configure.ac")
+
     def setup_build_environment(self, env):
         env.append_flags("CFLAGS", self.compiler.cxx98_flag)