diff --git a/boards.txt b/boards.txt
index 54622cee208bef13b3b007c602a3ad779a1a83c5..5994ea408e56728f4d597075dfbed213db62e40d 100644
--- a/boards.txt
+++ b/boards.txt
@@ -40,3 +40,45 @@ arduino_zero.build.variant=arduino_zero
 arduino_zero.build.variant_system_lib=
 arduino_zero.build.vid=0x2341
 arduino_zero.build.pid=0x004d
+
+arduino_zero_bl_dbg.name=Arduino Zero with Bootloader (Programming Port)
+arduino_zero_bl_dbg.vid.0=0x03eb
+arduino_zero_bl_dbg.pid.0=0x2111
+arduino_zero_bl_dbg.upload.tool=bossac
+arduino_zero_bl_dbg.upload.protocol=sam-ba
+arduino_zero_bl_dbg.upload.maximum_size=262144
+arduino_zero_bl_dbg.upload.use_1200bps_touch=false
+arduino_zero_bl_dbg.upload.wait_for_upload_port=false
+arduino_zero_bl_dbg.upload.native_usb=false
+arduino_zero_bl_dbg.build.mcu=cortex-m0plus
+arduino_zero_bl_dbg.build.f_cpu=48000000L
+arduino_zero_bl_dbg.build.usb_product="Arduino Zero"
+arduino_zero_bl_dbg.build.board=SAM_ZERO
+arduino_zero_bl_dbg.build.core=arduino
+arduino_zero_bl_dbg.build.extra_flags=-D__SAMD21G18A__ -mthumb {build.usb_flags}
+arduino_zero_bl_dbg.build.ldscript=linker_scripts/gcc/flash_with_bootloader.ld
+arduino_zero_bl_dbg.build.variant=arduino_zero
+arduino_zero_bl_dbg.build.variant_system_lib=
+arduino_zero_bl_dbg.build.vid=0x03eb
+arduino_zero_bl_dbg.build.pid=0x2111
+
+arduino_zero_bl.name=Arduino Zero with Bootloader (Native USB Port)
+arduino_zero_bl.vid.0=0x2341
+arduino_zero_bl.pid.0=0x004d
+arduino_zero_bl.upload.tool=bossac
+arduino_zero_bl.upload.protocol=sam-ba
+arduino_zero_bl.upload.maximum_size=262144
+arduino_zero_bl.upload.use_1200bps_touch=false
+arduino_zero_bl.upload.wait_for_upload_port=false
+arduino_zero_bl.upload.native_usb=true
+arduino_zero_bl.build.mcu=cortex-m0plus
+arduino_zero_bl.build.f_cpu=48000000L
+arduino_zero_bl.build.usb_product="Arduino Zero"
+arduino_zero_bl.build.board=SAM_ZERO
+arduino_zero_bl.build.core=arduino
+arduino_zero_bl.build.extra_flags=-D__SAMD21G18A__ -mthumb {build.usb_flags}
+arduino_zero_bl.build.ldscript=linker_scripts/gcc/flash_with_bootloader.ld
+arduino_zero_bl.build.variant=arduino_zero_bl
+arduino_zero_bl.build.variant_system_lib=
+arduino_zero_bl.build.vid=0x2341
+arduino_zero_bl.build.pid=0x004d
diff --git a/platform.txt b/platform.txt
index fc960227549e1cf53ee8694ec87efe2d9a5b76ec..af603be8cd043e6ac23c48b52f8d1f4c7cd75884 100644
--- a/platform.txt
+++ b/platform.txt
@@ -31,7 +31,7 @@ compiler.define=-DARDUINO=
 build.extra_flags=
 
 
-compiler.libsam.c.flags="-I{build.system.path}/libsamd" "-I{build.system.path}/CMSIS/CMSIS/Include/" "-I{build.system.path}/CMSIS/Device/ATMEL/"
+compiler.arm.cmsis.path="-I{runtime.ide.path}/hardware/tools/CMSIS/CMSIS/Include/" "-I{runtime.ide.path}/hardware/tools/CMSIS/Device/ATMEL/"
 
 # USB Flags
 # ---------
@@ -46,10 +46,10 @@ build.usb_manufacturer="Unknown"
 # ---------------------
 
 ## Compile c files
-recipe.c.o.pattern="{compiler.path}{compiler.c.cmd}" {compiler.c.flags} -mcpu={build.mcu} -DF_CPU={build.f_cpu} -DARDUINO={runtime.ide.version} -DARDUINO_{build.board} -DARDUINO_ARCH_{build.arch} {build.extra_flags} {compiler.libsam.c.flags} {includes} "{source_file}" -o "{object_file}"
+recipe.c.o.pattern="{compiler.path}{compiler.c.cmd}" {compiler.c.flags} -mcpu={build.mcu} -DF_CPU={build.f_cpu} -DARDUINO={runtime.ide.version} -DARDUINO_{build.board} -DARDUINO_ARCH_{build.arch} {build.extra_flags} {compiler.arm.cmsis.path} {includes} "{source_file}" -o "{object_file}"
 
 ## Compile c++ files
-recipe.cpp.o.pattern="{compiler.path}{compiler.cpp.cmd}" {compiler.cpp.flags} -mcpu={build.mcu} -DF_CPU={build.f_cpu} -DARDUINO={runtime.ide.version} -DARDUINO_{build.board} -DARDUINO_ARCH_{build.arch} {build.extra_flags} {compiler.libsam.c.flags} {includes} "{source_file}" -o "{object_file}"
+recipe.cpp.o.pattern="{compiler.path}{compiler.cpp.cmd}" {compiler.cpp.flags} -mcpu={build.mcu} -DF_CPU={build.f_cpu} -DARDUINO={runtime.ide.version} -DARDUINO_{build.board} -DARDUINO_ARCH_{build.arch} {build.extra_flags} {compiler.arm.cmsis.path} {includes} "{source_file}" -o "{object_file}"
 
 ## Create archives
 recipe.ar.pattern="{compiler.path}{compiler.ar.cmd}" {compiler.ar.flags} "{build.path}/{archive_file}" "{object_file}"