diff --git a/src/python/espressomd/CMakeLists.txt b/src/python/espressomd/CMakeLists.txt
index dca8bf8..78546ae 100644
--- a/src/python/espressomd/CMakeLists.txt
+++ b/src/python/espressomd/CMakeLists.txt
@@ -28,8 +28,8 @@ include_directories(${CMAKE_BINARY_DIR}/src)
 include_directories(${CMAKE_SOURCE_DIR}/src/core)
 include_directories(${CMAKE_BINARY_DIR}/src/core)
 if (HDF5_FOUND)
-    include_directories(${CMAKE_BINARY_DIR}/src/core/io/writer/h5md)
-    include_directories(${CMAKE_SOURCE_DIR}/src/core/io/writer/h5md)
+    include_directories(${CMAKE_BINARY_DIR}/src/core/io_/writer/h5md)
+    include_directories(${CMAKE_SOURCE_DIR}/src/core/io_/writer/h5md)
 endif(HDF5_FOUND)
 
 add_executable(gen_pxiconfig gen_pxiconfig.cpp)
@@ -60,7 +60,7 @@ file(GLOB cython_AUX *.py)
 file(COPY MDA_ESP DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
 SET(cython_AUX  "${cython_AUX}" CACHE INTERNAL "cython_AUX")
 
-add_subdirectory(io)
+add_subdirectory(io_)
 
 list(APPEND cython_SRC ${CMAKE_CURRENT_BINARY_DIR}/code_info.pyx)
 list(REMOVE_DUPLICATES cython_SRC)
diff --git a/src/python/espressomd/io/CMakeLists.txt b/src/python/espressomd/io/CMakeLists.txt
index 65ac3f7..bc3bf38 100644
--- a/src/python/espressomd/io/CMakeLists.txt
+++ b/src/python/espressomd/io/CMakeLists.txt
@@ -1,3 +1,3 @@
 configure_file(mpiio.py mpiio.py COPYONLY)
 add_subdirectory(writer)
-SET(cython_AUX  ${cython_AUX} "${CMAKE_SOURCE_DIR}/src/python/espressomd/io/__init__.py" CACHE INTERNAL "cython_AUX" FORCE)
+SET(cython_AUX  ${cython_AUX} "${CMAKE_SOURCE_DIR}/src/python/espressomd/io_/__init__.py" CACHE INTERNAL "cython_AUX" FORCE)