diff --git a/Tools/scripts/uploader.py b/Tools/scripts/uploader.py
index 36a653332e..857b06bcff 100755
--- a/Tools/scripts/uploader.py
+++ b/Tools/scripts/uploader.py
@@ -205,10 +205,17 @@ class uploader(object):
     NSH_INIT        = bytearray(b'\x0d\x0d\x0d')
     NSH_REBOOT_BL   = b"reboot -b\n"
     NSH_REBOOT      = b"reboot\n"
-    MAVLINK_REBOOT_ID1 = bytearray(b'\xfe\x21\x72\xff\x00\x4c\x00\x00\x40\x40\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\xf6\x00\x01\x00\x00\x53\x6b')
-    MAVLINK_REBOOT_ID0 = bytearray(b'\xfe\x21\x45\xff\x00\x4c\x00\x00\x40\x40\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\xf6\x00\x00\x00\x00\xcc\x37')
 
-    def __init__(self, portname, baudrate_bootloader, baudrate_flightstack, baudrate_bootloader_flash=None):
+    def __init__(self, portname, baudrate_bootloader, baudrate_flightstack, baudrate_bootloader_flash=None, target_system=None, target_component=None, source_system=None, source_component=None):
+        self.MAVLINK_REBOOT_ID1 = bytearray(b'\xfe\x21\x72\xff\x00\x4c\x00\x00\x40\x40\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\xf6\x00\x01\x00\x00\x53\x6b')
+        self.MAVLINK_REBOOT_ID0 = bytearray(b'\xfe\x21\x45\xff\x00\x4c\x00\x00\x40\x40\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\xf6\x00\x00\x00\x00\xcc\x37')
+        if target_component is None:
+            target_component = 1
+        if source_system is None:
+            source_system = 255
+        if source_component is None:
+            source_component = 1
+
         # open the port, keep the default timeout short so we can poll quickly
         self.port = serial.Serial(portname, baudrate_bootloader, timeout=1.0)
         self.otp = b''
@@ -220,6 +227,26 @@ class uploader(object):
             self.baudrate_bootloader_flash = self.baudrate_bootloader
         self.baudrate_flightstack = baudrate_flightstack
         self.baudrate_flightstack_idx = -1
+        # generate mavlink reboot message:
+        if target_system is not None:
+            from pymavlink import mavutil
+            m = mavutil.mavlink.MAVLink_command_long_message(
+                target_system,
+                target_component,
+                mavutil.mavlink.MAV_CMD_PREFLIGHT_REBOOT_SHUTDOWN,
+                1, # confirmation
+                3, # remain in bootloader
+                0,
+                0,
+                0,
+                0,
+                0,
+                0)
+            mav = mavutil.mavlink.MAVLink(self,
+                                          srcSystem=source_system,
+                                          srcComponent=source_component)
+            self.MAVLINK_REBOOT_ID1 = m.pack(mav)
+            self.MAVLINK_REBOOT_ID0 = None
 
     def close(self):
         if self.port is not None:
@@ -610,8 +637,10 @@ class uploader(object):
         try:
             # try MAVLINK command first
             self.port.flush()
-            self.__send(uploader.MAVLINK_REBOOT_ID1)
-            self.__send(uploader.MAVLINK_REBOOT_ID0)
+            if self.MAVLINK_REBOOT_ID1 is not None:
+                self.__send(self.MAVLINK_REBOOT_ID1)
+            if self.MAVLINK_REBOOT_ID0 is not None:
+                self.__send(self.MAVLINK_REBOOT_ID0)
             # then try reboot via NSH
             self.__send(uploader.NSH_INIT)
             self.__send(uploader.NSH_REBOOT_BL)
@@ -705,6 +734,10 @@ def main():
     parser.add_argument('--baud-flightstack', action="store", default="57600", help="Comma-separated list of baud rate of the serial port (default is 57600) when communicating with flight stack (Mavlink or NSH), only required for true serial ports.")
     parser.add_argument('--force', action='store_true', default=False, help='Override board type check and continue loading')
     parser.add_argument('--boot-delay', type=int, default=None, help='minimum boot delay to store in flash')
+    parser.add_argument('--target-system', type=int, action="store", help="System ID to update")
+    parser.add_argument('--target-component', type=int, action="store", help="Component ID to update")
+    parser.add_argument('--source-system', type=int, action="store", help="Source system to send reboot mavlink packets from", default=255)
+    parser.add_argument('--source-component', type=int, action="store", help="Source component to send reboot mavlink packets from", default=0)
     parser.add_argument('firmware', action="store", help="Firmware file to be uploaded")
     args = parser.parse_args()
 
@@ -731,7 +764,11 @@ def main():
                     up = uploader(port,
                                   args.baud_bootloader,
                                   baud_flightstack,
-                                  args.baud_bootloader_flash)
+                                  args.baud_bootloader_flash,
+                                  args.target_system,
+                                  args.target_component,
+                                  args.source_system,
+                                  args.source_component)
 
                 except Exception as e:
                     print("Exception creating uploader: %s" % str(e))