diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 56715c63..a84726da 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -131,9 +131,9 @@ else ()
 endif ()
 
 target_link_libraries(mmseqs-framework tinyexpr ${ZSTD_LIBRARIES} microtar)
-if (CYGWIN)
-    target_link_libraries(mmseqs-framework nedmalloc)
-endif ()
+# if (CYGWIN)
+#     target_link_libraries(mmseqs-framework nedmalloc)
+# endif ()
 
 if (EMSCRIPTEN)
     target_compile_definitions(mmseqs-framework PUBLIC -DHAVE_ZLIB=1 -DHAVE_BZLIB=1)