Aggressive rooster

I too think this is your roo asserting himself, having grown into his role. Because she used to be the dominant in the flock, he is targeting her especially. If you don't want to just let it play out (it will settle down, the faster the less you intervene), and you don't want to get rid of him, I would separate her for a few days; she will drop down the pecking order while getting relief from his attention, and hopefully he will have settled into his dominance and perceive her as less of a threat when she comes back.

When i put her in the nest box he managed to get close enough to peck her head. She has lost the feathers around her comb and her comb is a little bit bloody (albeit dried blood). She even crammed herself underneath the feeder and he had a go at her
 
Maybe you can confine the flock 2 hours before sunset and let the hen free range for a while too?
Well, for 2 hours it's not possible but for half an hour or so yes I can. Sunset is at 6pm at the moment and i usually get to where they are at about 5.
 
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For whatever reason he has decided to view her as competition rather than as a mate. Generally when this happens it escalates to the point where the two can no longer coexist. It is not impossible that he might kill her. It is very likely that you may have to rehome either the hen or the rooster. Monitor him as sometimes this escalates to abuse against other hens. This has been my experience only - hope that things work out for you.
 
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I had something similar happen last spring. I had two older gals and slowly introduced a few tribes. The older gals were the bosses. I had three cockerels. Everything was fine for quite some time until one day we found one of the older gals with her comb literally ripped off. She was brought into the house until she healed. When we introduced back into the flock, she was again attacked by one of the cockerels. My husband divided the coop permanently and the two older gals are together now and so far so good.
 
Having plenty of space, multiple feeders, and places to get away from bullying behaviors can all make a difference. See if this separation helps, although i don't think it's likely to matter very much.
If this cockerel is actually causing injuries, he'd be gone here! I love having roosters, but not any that hurt flockmates or attack humans.
If this hen is not available to him, is he going to pick on someone else? That would be the end of his happy home if he was here.
Mary
 
Update. Things are back to normal. I kept him separate for 6 days, letting him free range with the hens under supervision. She kept using me as a shield. Last Friday I realised that there was a sort of uncomfortable truce so I didn't separate him when they went back into the run. She panicked a bit but climbed onto the highest perch and was safe there. As darkness fell, he went into the coop first as he always does, followed by her. It was there that I realised that this was a game of dominance. she is the Alpha hen. When the other hens went in to roost (she's a golden comet, they're sussex or delawares, not entirely sure), she pecked each one in the head. since then, everything has been ok.
 
Hi. I have a small flock of 3 sussex hens (or perhaps sussex cross breeds), a golden comet hen and a Maltese black rooster (pretty rare breed and endemic to Malta (where I come from)). They have lived in harmony since the end of May when I got them as pullets. The golden comet quickly placed herself at the top of the pecking order and for the first few days the rooster was submissive to her too. Within 2 weeks they were pretty inseperable. two days ago, I cannot understand what happened. The rooster mounted her aggressively (more aggressive than he usually does) and pecked at her comb. when I let them out to free range I saw some dried blood on her comb. Throughout the rest of the day, whenever he saw her, he chased her and attacked her. when she could get away, she did, when she couldn't, she'd crouch down and keep her head down.

That evening, she wouldn't get into the coop so I put her in myself and he attacked her immediately so I isolated him by keeping him in the run at night and locked the girls up in the coop. Yesterday morning at 6 a.m. the coop door opened automatically (it has a hentronix door opener installed) and he got inside and attacked her again. I let them freerange for the whole day and he took a few swoops at her but only when she dared get close. In the evening I put her inside the run and she kept her distance (perhaps 2 feet) from the rest of them while they were having their bran mash and scratched around and pecked at the ground normally. He suddenly charged at her and pinned her down again. i separated them and knocked up a quick coop out of a wooden box to keep one of them in it for the night. At first I thought i was wise to keep the hen apart but as darkness fell she got agitated, knocked over the feeder and kept trying to get out. i got mad so I gabbed hold of him, put him in the makeshift coop even though it's a little bit low for him and put her in with the hens. He complained for a couple of minutes and settled down. I checked on them early this morning and all seems to be quiet (they're still separated of course but can see each other through the wire).

Do you think that this is a temporary phase, or once he has turned aggressive towards her, he will remain so? it seems as though he is thinking that she is a threat to the rest of the flock and doesn't want her there. At the moment I am mad enough at him to slaughter him even though I've never killed anything before. I'm going to exercise some patience till the end of the week and if he remains agressive, he'll get the chop.

One final thing. The hen was never the friendliest, in fact she was my least favourite but since Saturday, she has been climbing onto my dad's lap or onto my arm as though seeking solace. Is this behaviour normal?
Any rooster of any breed can become aggressive just like any rooster of any breed can become a teddy bear. Aggression typically occurs in cockerels as they reach puberty, generally at any time after four months of age.
 

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