Just to elaborate on this:
As you know tht there are two encapsulation methods availaible for trunk:
ISL is cisco properatory and its going off now.
802.1 Q is the open standard and its been used/deployed everywere.
Trunks are used to carry traffic that belongs to multiple VLANs between devices over the same link. A device can determine which VLAN the traffic belongs to by its VLAN identifier. The VLAN identifier is a tag that is encapsulated with the data. ISL and 802.1Q are two types of encapsulation that are used to carry data from multiple VLANs over trunk links.
ISL is a Cisco proprietary protocol for the interconnection of multiple switches and maintenance of VLAN information as traffic goes between switches. ISL provides VLAN trunking capabilities while it maintains full wire-speed performance on Ethernet links in full-duplex or half-duplex mode. ISL operates in a point-to-point environment and can support up to 1000 VLANs. In ISL, the original frame is encapsulated and an additional header is added before the frame is carried over a trunk link. At the receiving end, the header is removed and the frame is forwarded to the assigned VLAN. ISL uses Per VLAN Spanning Tree (PVST), which runs one instance of Spanning Tree Protocol (STP) per VLAN. PVST allows the optimization of root switch placement for each VLAN and supports the load balancing of VLANs over multiple trunk links.
802.1Q is the IEEE standard for tagging frames on a trunk and supports up to 4096 VLANs. In 802.1Q, the trunking device inserts a 4-byte tag into the original frame and recomputes the frame check sequence (FCS) before the device sends the frame over the trunk link. At the receiving end, the tag is removed and the frame is forwarded to the assigned VLAN. 802.1Q does not tag frames on the native VLAN. It tags all other frames that are transmitted and received on the trunk. When you configure an 802.1Q trunk, you must make sure that you configure the same native VLAN on both sides of the trunk. IEEE 802.1Q defines a single instance of spanning tree that runs on the native VLAN for all the VLANs in the network. This is called Mono Spanning Tree (MST). This lacks the flexibility and load balancing capability of PVST that is available with ISL. However, PVST+ offers the capability to retain multiple spanning tree topologies with 802.1Q trunking.
Hope this helps.