This post will show you how to configure a trunk port with a native vlan. In this specific example I am configuring a range of ports, but the commands for an individual interface will be the same once you have entered the config for a particular port.

First enter configuration mode

s3560#conf terminal

Now we configure the range of ports. Here we are configuring the range of ports to be a trunk, using dot1q encapsulation. We are allowing vlans 96-99, and vlan 101. We are also setting vlan101 to be the native vlan (no vlan tagging required).

s3560(config)#interface range gigabitEthernet 0/13 – 24
s3560(config-if-range)#description generic trunk ports
s3560(config-if-range)#switchport trunk encapsulation dot1q
s3560(config-if-range)#switchport mode trunk
s3560(config-if-range)#switchport trunk native vlan 101
s3560(config-if-range)switchport trunk allowed vlan 96-99,101

Now we enable spanning-tree portfast and bpduguard

s3560(config-if-range)#spanning-tree portfast

%Warning: portfast should only be enabled on ports connected to a single
host. Connecting hubs, concentrators, switches, bridges, etc… to this
interface when portfast is enabled, can cause temporary bridging loops.
Use with CAUTION

%Portfast will be configured in 13 interfaces due to the range command
but will only have effect when the interfaces are in a non-trunking mode.

s3560(config-if-range)#spanning-tree bpduguard enable
s3560(config-if-range)#end

Save your config changes

s3560#copy run start
Destination filename [startup-config]?
Building configuration…
[OK]
0 bytes copied in 1.443 secs (0 bytes/sec)
s3560#