Q:

Behavior about 802.1D with ISL

Reading this quote,

The 802.1Q standard defines one unique Spanning Tree instance to be used by all VLANs in the network.
STP runs on the Native VLAN so that it can communicate with both 802.1Q and non-802.1Q compatible switches.

This questions is based on 802.1D standard, How would be the behavior between two switches with ISL encapsulation, once which ISL doesn't support Native VLAN?
Beside, using ISL instead of 802.1Q, that won't disrespect the first statement?

A:

The first statement deals with 802.1Q, not ISL which is a different protocol, so the first statement has no relationship to ISL. Two switches connected with ISL will not have a Native VLAN because they don't use 802.1Q.
802.1Q has the concept of a native (untagged VLAN) because it inserts a VLAN tag inside the layer-2 frame for tagged VLANs, but just leaves the layer-2 frame alone for untagged (native) VLANs.
ISL encapsulates a layer-2 frame inside an ISL frame for all VLANs, so there is not an untagged (native) VLAN. Each VLAN uses ISL frame encapsulation and runs a separate STP (802.1d) instance.
Maybe you are confusing 802.1Q (tagging) with 802.1d (STP)?
This link has a chart comparing 802.1Q, PVST, and PVST+ which may help clarify this for you.

