diff --git a/CMakeLists.txt b/CMakeLists.txt
index 9c1b15041..aff40558e 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -218,24 +218,69 @@ include_directories(
 # as system headers.
 include_directories(SYSTEM ${EIGEN_INCLUDE_DIRS})
 
+
+set(THEIA_USE_SYSTEM_CEREAL OFF CACHE BOOL "Use a system Cereal library")
+set(THEIA_USE_SYSTEM_FLANN OFF CACHE BOOL "Use a system Flann library")
+
+include_directories(libraries)
+
 # build Third party libraries included in distro.
-add_subdirectory(libraries)
-include_directories(
-  libraries
-  libraries/spectra
-  ${akaze_SOURCE_DIR}
-  ${akaze_INCLUDE_DIR}
-  ${cereal_SOURCE_DIR}
-  ${cereal_SOURCE_DIR}/include
-  ${flann_SOURCE_DIR}
-  ${flann_SOURCE_DIR}/src/cpp
-  ${gtest_SOURCE_DIR}/include
-  ${gtest_SOURCE_DIR}
-  ${optimo_SOURCE_DIR}
-  ${statx_SOURCE_DIR}
-  ${stlplus3_SOURCE_DIR}
-  ${vlfeat_SOURCE_DIR}
-  ${visual_sfm_SOURCE_DIR})
+if (${BUILD_TESTING})
+  add_subdirectory(libraries/gtest)
+endif (${BUILD_TESTING})
+
+# AKAZE feature extractor.
+add_subdirectory(libraries/akaze)
+
+include_directories(${akaze_SOURCE_DIR} ${akaze_INCLUDE_DIR})
+
+# Cereal for portable IO.
+if(NOT THEIA_USE_SYSTEM_CEREAL)
+  add_subdirectory(libraries/cereal)
+
+  include_directories(${cereal_SOURCE_DIR} ${cereal_SOURCE_DIR}/include)
+else()
+  find_package(cereal REQUIRED)
+
+  set(_THEIA_CEREAL_LIBRARIES cereal)
+endif()
+
+# Flann for fast approximate nearest neighbor searches.
+if(NOT THEIA_USE_SYSTEM_FLANN)
+  add_subdirectory(libraries/flann)
+
+  include_directories(${flann_SOURCE_DIR} ${flann_SOURCE_DIR}/src/cpp)
+  set(_THEIA_FLANN_LIBRARIES flann_cpp)
+else()
+  find_package(Flann REQUIRED)
+
+  include_directories(${FLANN_INCLUDE_DIR})
+  set(_THEIA_FLANN_LIBRARIES ${FLANN_LIBRARY})
+endif()
+
+# Add Optimo.
+add_subdirectory(libraries/optimo)
+include_directories(${optimo_SOURCE_DIR})
+
+# Add Spectra.
+include_directories(libraries/spectra)
+
+# Add Statx.
+add_subdirectory(libraries/statx)
+include_directories(${statx_SOURCE_DIR})
+
+# STLPlus for filepath tools.
+add_subdirectory(libraries/stlplus3)
+include_directories(${stlplus3_SOURCE_DIR})
+
+# Add VLFeat.
+add_subdirectory(libraries/vlfeat)
+include_directories(${vlfeat_SOURCE_DIR})
+
+# Add VisualSfM files.
+add_subdirectory(libraries/visual_sfm)
+include_directories(${visual_sfm_SOURCE_DIR})
+
 
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake")
 include(OptimizeTheiaCompilerFlags)
diff --git a/cmake/FindFlann.cmake b/cmake/FindFlann.cmake
new file mode 100644
index 000000000..5d19ef75f
--- /dev/null
+++ b/cmake/FindFlann.cmake
@@ -0,0 +1,63 @@
+###############################################################################
+# Find FLANN
+#
+# This sets the following variables:
+# FLANN_FOUND - True if FLANN was found.
+# FLANN_INCLUDE_DIRS - Directories containing the FLANN include files.
+# FLANN_LIBRARIES - Libraries needed to use FLANN.
+# FLANN_DEFINITIONS - Compiler flags for FLANN.
+# If FLANN_USE_STATIC is specified and then look for static libraries ONLY else
+# look for shared ones
+
+if(FLANN_USE_STATIC)
+  set(FLANN_RELEASE_NAME flann_cpp_s flann_cpp)
+  set(FLANN_DEBUG_NAME flann_cpp_s-gd flann_cpp-gd)
+else(FLANN_USE_STATIC)
+  set(FLANN_RELEASE_NAME flann_cpp)
+  set(FLANN_DEBUG_NAME flann_cpp-gd)
+endif(FLANN_USE_STATIC)
+
+find_package(PkgConfig QUIET)
+if (FLANN_FIND_VERSION)
+    pkg_check_modules(PC_FLANN flann>=${FLANN_FIND_VERSION})
+else(FLANN_FIND_VERSION)
+    pkg_check_modules(PC_FLANN flann)
+endif(FLANN_FIND_VERSION)
+
+set(FLANN_DEFINITIONS ${PC_FLANN_CFLAGS_OTHER})
+
+find_path(FLANN_INCLUDE_DIR flann/flann.hpp
+          HINTS ${PC_FLANN_INCLUDEDIR} ${PC_FLANN_INCLUDE_DIRS} "${FLANN_ROOT}" "$ENV{FLANN_ROOT}"
+          PATHS "$ENV{PROGRAMFILES}/Flann" "$ENV{PROGRAMW6432}/Flann"
+          PATH_SUFFIXES include)
+
+find_library(FLANN_LIBRARY
+             NAMES ${FLANN_RELEASE_NAME}
+             HINTS ${PC_FLANN_LIBDIR} ${PC_FLANN_LIBRARY_DIRS} "${FLANN_ROOT}" "$ENV{FLANN_ROOT}"
+             PATHS "$ENV{PROGRAMFILES}/Flann" "$ENV{PROGRAMW6432}/Flann"
+	     PATH_SUFFIXES lib)
+
+find_library(FLANN_LIBRARY_DEBUG
+             NAMES ${FLANN_DEBUG_NAME} ${FLANN_RELEASE_NAME}
+	     HINTS ${PC_FLANN_LIBDIR} ${PC_FLANN_LIBRARY_DIRS} "${FLANN_ROOT}" "$ENV{FLANN_ROOT}"
+	     PATHS "$ENV{PROGRAMFILES}/Flann" "$ENV{PROGRAMW6432}/Flann"
+	     PATH_SUFFIXES lib)
+
+if(NOT FLANN_LIBRARY_DEBUG)
+  set(FLANN_LIBRARY_DEBUG ${FLANN_LIBRARY})
+endif(NOT FLANN_LIBRARY_DEBUG)
+
+set(FLANN_INCLUDE_DIRS ${FLANN_INCLUDE_DIR})
+set(FLANN_LIBRARIES optimized ${FLANN_LIBRARY} debug ${FLANN_LIBRARY_DEBUG})
+
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(FLANN DEFAULT_MSG FLANN_LIBRARY FLANN_INCLUDE_DIR)
+
+mark_as_advanced(FLANN_LIBRARY FLANN_LIBRARY_DEBUG FLANN_INCLUDE_DIR)
+
+if(FLANN_FOUND)
+  message(STATUS "Flann found (include: ${FLANN_INCLUDE_DIRS}, lib: ${FLANN_LIBRARIES})")
+  if(FLANN_USE_STATIC)
+    add_definitions(-DFLANN_STATIC)
+  endif(FLANN_USE_STATIC)
+endif(FLANN_FOUND)
diff --git a/libraries/CMakeLists.txt b/libraries/CMakeLists.txt
deleted file mode 100644
index 84f38298e..000000000
--- a/libraries/CMakeLists.txt
+++ /dev/null
@@ -1,27 +0,0 @@
-if (${BUILD_TESTING})
-  add_subdirectory(gtest)
-endif (${BUILD_TESTING})
-
-# AKAZE feature extractor.
-add_subdirectory(akaze)
-
-# Cereal for portable IO.
-add_subdirectory(cereal)
-
-# Flann for fast approximate nearest neighbor searches.
-add_subdirectory(flann)
-
-# Add Optimo.
-add_subdirectory(optimo)
-
-# Add Statx.
-add_subdirectory(statx)
-
-# STLPlus for filepath tools.
-add_subdirectory(stlplus3)
-
-# Add VLFeat.
-add_subdirectory(vlfeat)
-
-# Add VisualSfM files.
-add_subdirectory(visual_sfm)
\ No newline at end of file
diff --git a/src/theia/CMakeLists.txt b/src/theia/CMakeLists.txt
index 65787eb51..07c54a421 100644
--- a/src/theia/CMakeLists.txt
+++ b/src/theia/CMakeLists.txt
@@ -174,14 +174,15 @@ set(THEIA_LIBRARY_DEPENDENCIES
   ${CERES_LIBRARIES}
   ${GFLAGS_LIBRARIES}
   ${GLOG_LIBRARIES}
-  ${SUITESPARSE_LIBRARIES}
   ${OPENIMAGEIO_LIBRARIES}
+  ${SUITESPARSE_LIBRARIES}
+  ${_THEIA_CEREAL_LIBRARIES}
+  ${_THEIA_FLANN_LIBRARIES}
   akaze
-  flann_cpp
   statx
   stlplus3
-  vlfeat
-  visual_sfm)
+  visual_sfm
+  vlfeat)
 
 set(THEIA_LIBRARY_SOURCE
   ${THEIA_SRC}