diff --git a/CMakeLists.txt b/CMakeLists.txt
index 2b6584d3..205e78a0 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -321,7 +321,7 @@ if (BUILDDOC)
       ${DOXYGEN_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile
       COMMAND tar -czf html/xml.tar.gz -C xml .
       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-      COMMENT "Generating API documentation with Doxygen" VERBATIM
+      COMMENT "Generating C/C++ API documentation with Doxygen" VERBATIM
     )
   else ()
     message (SEND_ERROR "ERROR - Failed to find a compatible version of Doxygen. API doc will not be generated")
@@ -330,6 +330,10 @@ if (BUILDDOC)
   # Check if Sphinx is installed and add target to generate API documentation
   # Currently, the per-module documentation for python is generated from the
   # python2 modules.
+  # Since python2 is required for documentation, only copy from python2 paths, this
+  # ensures that sphinx doesn't run across python2 and python3 binaries.  When running
+  # the sphinx tools, explicitly run from the python2 interpreter (tested with the sphinx
+  # 1.3.6 python2 and python3 modules).
   if(BUILDSWIGPYTHON)
     find_package (Sphinx 1.3 REQUIRED)
     if (SPHINX_FOUND AND SPHINX_VERSION VERSION_GREATER "1.3")
@@ -337,16 +341,16 @@ if (BUILDDOC)
       configure_file (${CMAKE_CURRENT_SOURCE_DIR}/doxy/index.rst ${CMAKE_CURRENT_BINARY_DIR}/pydoc/index.rst COPYONLY)
       add_custom_target (pydoc ALL
         COMMAND rm -r -f ${CMAKE_BINARY_DIR}/pyupm && mkdir -p ${CMAKE_BINARY_DIR}/pyupm
-        COMMAND find ${CMAKE_BINARY_DIR}/src -name "_pyupm_*.so" -exec cp {} ${CMAKE_BINARY_DIR}/pyupm \;
-        COMMAND find ${CMAKE_BINARY_DIR}/src -name "pyupm_*.py" -exec cp {} ${CMAKE_BINARY_DIR}/pyupm \;
-        COMMAND ${SPHINX_API_EXECUTABLE} -f -o pydoc  ${CMAKE_BINARY_DIR}/pyupm
+        COMMAND find ${CMAKE_BINARY_DIR}/src -path "*python${MIN_VER_PYTHON2}/_pyupm_*.so" -exec cp {} ${CMAKE_BINARY_DIR}/pyupm \;
+        COMMAND find ${CMAKE_BINARY_DIR}/src -path "*python${MIN_VER_PYTHON2}/pyupm_*.py" -exec cp {} ${CMAKE_BINARY_DIR}/pyupm \;
+        COMMAND ${PYTHON2_EXECUTABLE} ${SPHINX_API_EXECUTABLE} -f -o pydoc  ${CMAKE_BINARY_DIR}/pyupm
         # TODO: use a separate cmake FILE module for string replacement instead
-        COMMAND ${SPHINX_EXECUTABLE} -b html pydoc html/python
+        COMMAND ${PYTHON2_EXECUTABLE} ${SPHINX_EXECUTABLE} -b html pydoc html/python
         COMMAND sed -i.bak s|\">pyupm_|\">|g html/python/index.html html/python/modules.html
         COMMAND sed -i.bak s|[[:space:]][mM]odule</a>|</a>|g html/python/index.html html/python/modules.html
         DEPENDS doc
         WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-        COMMENT "Generating API documentation with Sphinx" VERBATIM
+        COMMENT "Generating Python API documentation with Sphinx" VERBATIM
       )
     else ()
       message (SEND_ERROR "ERROR - Failed to find a compatible version of Sphinx. Python API doc will not be generated")
@@ -363,7 +367,7 @@ if (BUILDDOC)
         COMMAND ${CMAKE_SOURCE_DIR}/doxy/doxygen2jsdoc/tolower.js -i html/node
         DEPENDS doc
         WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-        COMMENT "Generating API documentation with Yuidoc" VERBATIM
+        COMMENT "Generating Javascript API documentation with Yuidoc" VERBATIM
       )
     else ()
       message (SEND_ERROR "ERROR - Failed to find a compatible version of Yuidoc. Node.js API doc will not be generated")
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index bbb91782..858e005a 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -510,13 +510,6 @@ function(upm_swig_java)
   endif (NOT ";${JAVASWIG_BLACKLIST};" MATCHES ";${libname};")
 endfunction(upm_swig_java)
 
-macro(upm_doxygen)
-  if (DOXYGEN_FOUND)
-    set (CMAKE_SWIG_FLAGS -DDOXYGEN=${DOXYGEN_FOUND})
-    add_dependencies (doc ${libname})
-  endif ()
-endmacro(upm_doxygen)
-
 if (NPM)
 add_custom_target (npmpkg)
 add_custom_command (TARGET npmpkg POST_BUILD COMMAND echo "Creating NPM tarballs..."
@@ -759,11 +752,6 @@ function(upm_module_init)
   set_target_properties(${libname} PROPERTIES PKG_EXT_REQ_LIBS "${reqlibname}")
   set_target_properties(${libname} PROPERTIES TARGET_BINARY_DIR "${CMAKE_CURRENT_BINARY_DIR}")
 
-  # Skip doxygen run on C (for now)
-  if (BUILDDOC AND NOT IS_C_LIBRARY)
-    upm_doxygen()
-  endif()
-
   # Install target library to lib dir
   install (TARGETS ${libname}
       DESTINATION ${LIB_INSTALL_DIR}