Aranas
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Here is another helpfull list: The Defenitive List of Markers.
They are quite numerous now!
The Defenitive List of Markers:
Exoskeleton Marker = Brown/Red Marker This Marker is used for the Mezzodemon Warmonger's Ability:
Exoskeleton
At the start of the game, place 1 copper Exoskeleton marker on a Mezzodemon Warmongers Army Card for each Mezzodemon Warmonger figure in your Army. After a Mezzodemon Warmonger rolls defense dice against a normal attack, you may remove 1 Exoskeleton marker from its Army Card to ignore all wounds inflicted by that attack.
Experience Marker = Purple Markers These Markers are used for the Tagawa Samuraï's Ability:
Bloodlust
For every opponent's figure a Tagawa Samurai destroys, place a purple Experience Marker on this card. When attacking with Tagawa Samurai, roll one additional attack die for each Experience Marker on this card. A maximum of 3 Experience Markers can be placed on this card.
Grenade Marker = White Marker This Marker is used for the Airborne Elite's Special Attack:
Grenade Special Attack
Range 5. Lob 12. Attack 2.
Use this power once per game. Start the game with a Grenade Marker on this card. Remove the Grenade Marker to throw grenades. One at a time do the following with each Airborne Elite: Choose a figure to attack. No clear line of sight is needed. Any figures adjacent to the chosen figure are also affected by the Grenade Special Attack. Roll 2 attack dice once for all affected figures. Each figure rolls defense dice separately.
If you look on the bottom of the Grenade Marker, it should have a little sticker with an image of a Grenade.
Lycanthropy Marker = Green Glow-in-the-Dark Marker This Marker is used for the Werewolf Lord's Ability:
Lycanthropy
This Werewolf Lord starts the game with 3 green Lycanthropy markers on its army card. If an opponent's unique hero receives at least 1 wound from this Werewolf Lord, you may place a Lycanthropy marker on that figure's army card. For the duration of the game, that figure loses its species, class, and personality. Instead, it has the following characteristics:
Negation Marker = Brown Markers These Markers are used for the Negation ability found on Nilrend's Negation Glyph from SotM and on Morsbane's card:
Rod of Negation
Start the game with 3 brown Negation Markers on this card. At the end of the turn, if you have at least 1 Negation Marker on this card, you may choose any opponent's unique figure within 6 clear sight spaces of Morsbane. Roll the 20-sided die. If you roll a 1-15, nothing happens. If you roll a 16-19, place a Negation Marker on the chosen figure's Army Card. All of that figure's special powers are negated for the entire game. If you roll a 20, destroy the chosen figure.
Glyph of Nilrend (Negation)
When one of your figures stops here, you may choose any opponent's figure. Roll the 20-sided die. If you roll a 1-4, nothing happens. If you roll a 5-20, place the Gold Negation Marker on the chosen figure's Army Card. All of that figure's special powers are negated for the rest of the game.
This translates to, whenever you Negate something, you put a Negation Marker on that something's Army Card.
Order Markers = Gray Shield (1, 2, 3 and X Markers) Order Markers enable players to plan and secretly record their planned moves for the entire round. By requiring the use of the Order Markers, players are forced to use logic and forethought when planning their strategy of what Figure(s) to move and when.
Round Marker = Black Marker This Marker is used to show what Round the game is currently on. There is a small Round Track near each Scenario with a limited number of Rounds (1-2-3-4-5-ect). After each Round is completed (no player has an Order Marker left standing) the Marker is moved one step forward on the Round Track and a new Round begins. This is to assist players in remembering the current Round in Scenarios where players have a limited amount of Turns (I.E., players must do a task before round 6 or lose).
Wound Marker = Maroon Markers These Markers are used to display how much Life a Hero has lost in the current battle.
Aranas
Thanks to CupidsArt (part of it is from one of CupidsArt's posts), to a lot of contributors and special thanks to Malechi.
They are quite numerous now!
The Defenitive List of Markers:

Exoskeleton Marker = Brown/Red Marker This Marker is used for the Mezzodemon Warmonger's Ability:
Exoskeleton
At the start of the game, place 1 copper Exoskeleton marker on a Mezzodemon Warmongers Army Card for each Mezzodemon Warmonger figure in your Army. After a Mezzodemon Warmonger rolls defense dice against a normal attack, you may remove 1 Exoskeleton marker from its Army Card to ignore all wounds inflicted by that attack.

Experience Marker = Purple Markers These Markers are used for the Tagawa Samuraï's Ability:
Bloodlust
For every opponent's figure a Tagawa Samurai destroys, place a purple Experience Marker on this card. When attacking with Tagawa Samurai, roll one additional attack die for each Experience Marker on this card. A maximum of 3 Experience Markers can be placed on this card.


Grenade Marker = White Marker This Marker is used for the Airborne Elite's Special Attack:
Grenade Special Attack
Range 5. Lob 12. Attack 2.
Use this power once per game. Start the game with a Grenade Marker on this card. Remove the Grenade Marker to throw grenades. One at a time do the following with each Airborne Elite: Choose a figure to attack. No clear line of sight is needed. Any figures adjacent to the chosen figure are also affected by the Grenade Special Attack. Roll 2 attack dice once for all affected figures. Each figure rolls defense dice separately.
If you look on the bottom of the Grenade Marker, it should have a little sticker with an image of a Grenade.

Lycanthropy Marker = Green Glow-in-the-Dark Marker This Marker is used for the Werewolf Lord's Ability:
Lycanthropy
This Werewolf Lord starts the game with 3 green Lycanthropy markers on its army card. If an opponent's unique hero receives at least 1 wound from this Werewolf Lord, you may place a Lycanthropy marker on that figure's army card. For the duration of the game, that figure loses its species, class, and personality. Instead, it has the following characteristics:
- Species: Hybrid
- Class: Hunter
- Personality: Tormented

Negation Marker = Brown Markers These Markers are used for the Negation ability found on Nilrend's Negation Glyph from SotM and on Morsbane's card:
Rod of Negation
Start the game with 3 brown Negation Markers on this card. At the end of the turn, if you have at least 1 Negation Marker on this card, you may choose any opponent's unique figure within 6 clear sight spaces of Morsbane. Roll the 20-sided die. If you roll a 1-15, nothing happens. If you roll a 16-19, place a Negation Marker on the chosen figure's Army Card. All of that figure's special powers are negated for the entire game. If you roll a 20, destroy the chosen figure.
Glyph of Nilrend (Negation)
When one of your figures stops here, you may choose any opponent's figure. Roll the 20-sided die. If you roll a 1-4, nothing happens. If you roll a 5-20, place the Gold Negation Marker on the chosen figure's Army Card. All of that figure's special powers are negated for the rest of the game.
This translates to, whenever you Negate something, you put a Negation Marker on that something's Army Card.

Order Markers = Gray Shield (1, 2, 3 and X Markers) Order Markers enable players to plan and secretly record their planned moves for the entire round. By requiring the use of the Order Markers, players are forced to use logic and forethought when planning their strategy of what Figure(s) to move and when.
Order Markers = Blue Shield (1, 2, 3 and X Markers) Same use. Found in Marvel Heroscape Master Set.
Order Markers = Dark Green Shield (1, 2, 3 and X Markers) Same use. Found in Swarm of the Marro Heroscape Master Set.
Order Markers = Purple Shield (1, 2, 3 and X Markers) Same use. Found in D&D Heroscape Master Set.

Round Marker = Black Marker This Marker is used to show what Round the game is currently on. There is a small Round Track near each Scenario with a limited number of Rounds (1-2-3-4-5-ect). After each Round is completed (no player has an Order Marker left standing) the Marker is moved one step forward on the Round Track and a new Round begins. This is to assist players in remembering the current Round in Scenarios where players have a limited amount of Turns (I.E., players must do a task before round 6 or lose).

Wound Marker = Maroon Markers These Markers are used to display how much Life a Hero has lost in the current battle.
Wound Marker = Red Markers Same use. Found in Marvel Heroscape Master Set.
Aranas
Thanks to CupidsArt (part of it is from one of CupidsArt's posts), to a lot of contributors and special thanks to Malechi.