he native vlan is a concept specific to an 802.1q trunk.

A trunk is a link over which multiple vlans can be sent. To distinguish between the vlans each frame is tagged
with it's vlan ID. The native vlan is the vlan on a trunk link that does not have a vlan ID tag in the frames.
You should make sure each end of the trunk agrees on what the native vlan is. It can be any vlan, Cisco best
practice is to pick an unused vlan and assign that as the native vlan.
The native vlan is needed when you connect to a switch that does not understand vlan tags and do it is really
for backwards compatability.
Jon
in a 802.1Q the native vlan is the vlan whose frames are sent out untagged without the 802.1Q tag.
The native vlan was thought as a way to provide backward compatibility to NICs that doesn't support 802.1Q
vlan tagging
You can use or not use the Native Vlan but what it is very important is that the native vlan must match on both
sides of the trunk or IP connectivity problems can occur.
on a switch interface:
switchport trunk native vlan X
on a router subif:
int f0/0.50
enc dot1q 5 native
the default native vlan is 1 on switches and routers.
Hope to help

Native VLAN Mismatches.

Error#1

Lets assume that one of the workstations on the network (PC 5) cannot
connect to the internal web server WEB/TFTP, lets use the figure below as an
example of a switched network, the first place you start will be at the Switch
2 to check if VLANs are properly configured. Looking at the diagram, switch

port fa0/3 on Switch 2 is configured as

atrunk port.
Native VLAN Mismatch

When you connect to switch S2, if there is an error on the switch port, it will appear on your
console window, in this case there is and it looks like this:
S2#
#CDP-4-NATIVE VLAN_MISMATCH: Native VLAN mismatch discovered on
FastEthernet0/3 (100), with S1 FastEthernet0/3 (99).
Using the show interfaces fa0/3 switchport command will display connectivity detail on
the port.
e.g
S2#showinterfacesfa0/3switchport
Name:fa0/3
Switchport:Enabled
AdministrativeMode:trunk
OperationalMode:trunk
AdministrativeTrunkingEncapsulation:dot1q
OperationalTrunkingEncapsulation:dot1q
NagotiationofTrunking:On
AccessModeVLAN:1(default)
TrunkingNativeModeVLAN:100(Inactive)

TrunkingVLANsEnabled:10,99

Looking at the above detail, you will notice that the native VLAN has been set to VLAN 100
and it is inactive.
As you look further down the output, you see that the allowed VLANs are 10 and 99.

To sum it up, this is a case of a mismatched native VLAN

The solution:
You need to reconfigure the native VLAN on the Fast Ethernet F0/3 trunk port to be VLAN
99. e.g
S2#config t
S2#interface fa0/3
S2#switchport trunk native vlan 99
S2#end
After you have done that, use the show interfaces fa0/3 switchport confirm you
configuration.
And use the Ping to confirm connectivity with the server. e.g.
PC5> ping 192.168.10.30
Pinging 192.168.10.30 with 32 bytes of data:
Reply from 192.168.10.30: bytes-32 times-147ms TT-128
Reply from 192.168.10.30: bytes-32 times-147ms TT-128
Reply from 192.168.10.30: bytes-32 times-147ms TT-128
...

The screen output for the computer PC5 shows that connectivity has been restored to the
WEB/TFTP server found at IP address 192.168.10.30.
- See more at: http://www.orbit-computer-solutions.com/Native-VLAN-Mismatches.php#sthash.IXYXTlNb.dpuf