Which protocol cisco is used for trunk?

802.1Q

VLAN Trunking Protocol (VTP) of Cisco Catalyst switches to simplify management of the VLAN database across multiple switches.

in adition open method to configure trunk we use IEEE802.1q mode in Cisco Switches as well

in cisco example  as  below

conf t

int fa0

switchport mode trunk

switchport trunk encapsulation dot1q

exit

when you want to allow  certain val in this  trunk use below

switchport trunk allowed vlan Number1, Number2

Inter-Switch Link (ISL), which is a Cisco proprietary protocol