I thought I read somewhere that Hunter's Quarry worked like a mark, but I can't find this in the rules. I've just recently started DMing 4e again and can't remember where I picked that up. It may have not been official, but I don't tend to remember non-official things. It looks as if it is not affected by the marking rules. Am I missing something or is it not written somewhere? I have the PHB and the last roll-up of Errata, but I can't find anything on the subject which means to me that they are not related and I could have a monster that is both marked and has HQ applied.
They work similarly but are different mechanics
The Marked condition says:
Marked is a condition.
- You take a −2 penalty to attack rolls for any attack that doesn't target the creature that marked you.
- You can be subjected only to one mark at a time. Newer marks supersede older ones.
- A mark ends when its creator dies or is unconscious.
While Hunter's Quarry says:
A ranger with the Hunter's Quarry class feature can, once per turn as a minor action, designate the nearest visible enemy as his or her quarry. This designation lasts until the encounter ends, the quarry is defeated, or the ranger designates a different target.
Once per round, the ranger deals 1d6 per tier damage when hitting his or her quarry with an attack. If the ranger can make multiple attacks in a round, the ranger decides which attack to apply the extra damage to after all the attacks are rolled.
As you can see, they both have similar wordings, but they are different things (condition vs class ability) and work differently. As such, a target can be both marked and targeted by Hunter's Quarry.
Not only that, but rangers can learn a daily power (at 9th level) that allows them to mark a target: Marked for Death. Which is probably what you had in mind.
Hunter's Quarry doesn't mark. Hunter's Mark quarries.
Linguistic drift is a real bear. Specifically, "mark" in its "to single out or destine" sense could apply to any number of abilities where a character expresses an interest in e.g. these 6 fish in particular.
So, in a surprising inversion of your original premise, you may actually be thinking that the 5E 1st-level ranger spell Hunter's Mark is quite similar to the 4E ranger class feature Hunter's Quarry. And, well, yes, it is. But it's nothing to do with the marked condition in either case.