diff --git a/.gitmodules b/.gitmodules
index 15d926da0d..c263bdf934 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -6,11 +6,11 @@
 	path = src/modules/uavcan/libuavcan
 	url = https://github.com/UAVCAN/libuavcan.git
 	branch = master
-[submodule "Tools/genmsg"]
+[submodule "msg/tools/genmsg"]
 	path = msg/tools/genmsg
 	url = https://github.com/ros/genmsg.git
 	branch = indigo-devel
-[submodule "Tools/gencpp"]
+[submodule "msg/tools/gencpp"]
 	path = msg/tools/gencpp
 	url = https://github.com/ros/gencpp.git
 	branch = indigo-devel
@@ -42,7 +42,7 @@
 	path = src/drivers/gps/devices
 	url = https://github.com/PX4/GpsDrivers.git
 	branch = master
-[submodule "src/lib/micro-CDR"]
+[submodule "src/modules/micrortps_bridge/micro-CDR"]
 	path = src/modules/micrortps_bridge/micro-CDR
 	url = https://github.com/eProsima/micro-CDR.git
 	branch = master