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When it gets to the point that there is actual physical injury, frayed fins, or the clown is no longer coming out to eat, breathing heavily in the corner it's time to intervene.
Female clowns will seem aggressive but normally the smaller one submits by shaking and the female goes about her business, if she is continually chasing the smaller clown that is an issue.
Sometimes a female rejects a male, who knows why. If you have a breeding box I would put the larger fish in the breeder box for 3-5 days if the situation gets any worse.
What kind of clown? I've heard that maroons can be very picky about potential mates.
It may just be because the clowns aren't closely related... if there is this much fighting between them at this stage, then they most likely won't pair up. Usually you want to stick with clowns that are visibly similar for the best chance of mating.

I have two maroons that I recently paired. I put one in an acclimation box for three days to relieve some initial aggression and then let him out. It worked well. There was almost no nipping because all aggression was defused while one was in the acclimation box.
How long have you had the clowns?
You may have added a transitioning female (the phantom), if that is the case then removal is really the only option if the tank is not large enough to house two females and provide enough room for any one fish to escape to another part of the tank.
Usually I would say let them work it out but you got different clowns at different times, it's impossible predict if the phantom was transitioning to a female. Clowns will fight, I have had female beat up on males, but that usually calms down in a couple days and never results in physical injury.
Have you tried move the rock work around?
)They'll be fine then. Just throw one in an acclimation box for three days and that should alleviate most of the initial aggression between them.
If you don't have an acclimation box you can easily make one out of Tupperware. Simply make outward holes in it so the clown doesn't scrap himself on them. Saves you $$

