CCIE 400-101: Layer 2 Technologies

IEEE 802.1Q (dot1q) is a industry standards based implementation of carrying traffic for multiple VLANs over a single trunk link between two Ethernet switches.
This means adding an identifier (tag) to frames to indicate what VLAN the frame belongs to.
802.1Q does not encapsulate the original frame. Instead, for Ethernet frames, it adds a 32-bit (4-byte) field between the source MAC address and the EtherType/Length fields of the original frame.

TPID - Tag Protocol Identifier (16 bits): set to a value of 0x8100 to identify the frame as an IEEE 802.1Q tagged frame.
Priority (3 bits): indicates the priority level (0 through 7) used for QoS.
CFI - Canonical Format Indicator (1 bit): specifies if the MAC address is in noncanonical (1) or canonical (0) format.
VID - VLAN Identifier (12 bits): uniquely identifies the VLAN which the frame belongs to.

In short, the ONLY difference between a regular VLAN and the native VLAN is that frames from/to the native VLAN are carried untagged.
As explained in dot1q section, VLANs are identified by adding a tag to the frame.
What happens if a trunk port receives a frame without this tag? Which VLAN does the frame belong to? Answer: the native VLAN.
If a switch receives an untagged frame, it associates that frame to the native VLAN.
When a switch sends out a frame belonging to the native VLAN, it removes the tag.
The native VLAN is configurable on a per port basis with the switchport trunk native vlan <vlan-id> command.
The default native VLAN is VLAN 1.

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