diff --git a/build-tools/downloadMafTools b/build-tools/downloadMafTools
index d1dc8fe7f..004d551fa 100755
--- a/build-tools/downloadMafTools
+++ b/build-tools/downloadMafTools
@@ -51,7 +51,7 @@ export HTSLIB_LIBS="$(pwd)/libhts.a -lbz2 -ldeflate -lm -lpthread -lz -llzma -pt
 cd ${mafBuildDir}
 git clone https://github.com/ComparativeGenomicsToolkit/taffy.git
 cd taffy
-git checkout 33a596a6fe168e0feb609fe9c458b9992b2ea090
+git checkout 5221c50fbf119699db1112ce74eea90dea17ba95
 git submodule update --init --recursive
 export HALDIR=${CWD}/submodules/hal
 make -j ${numcpu}