We have four guinea foul in our backyard flock. They are becoming increasingly aggressive toward ALL of our other birds. Is this characteristic of guineas? Should they be separated?
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So the Guineas fly over the fence into the chicken pen, instead of free ranging all day? Cover the pen...
Their behavior won't change, and it may even get worse now that breeding season is starting up. Separating them from the chickens is the only way to stop the aggression problem, by either doing what needs to be done to prevent them from getting in with the chickens at all from now on, or re-homing them. Sorry you are having issues. There are always workable solutions, tho they may not work for you/your situation.
Don't take offense to this, because I am not at all singling you out with this statement, a lot of people have issues with Guineas being aggressive towards their chickens, (so this is just a bit of general, helpful advise for anyone new to Guineas or thinking about getting Guineas who might read this thread) but... a little bit of homework done on Guinea behavior before adding them to a flock of chickens, and having a back up plan just in case there are issues is always helpful.