Yes females will mark, it's a sign of dominance. I've seen my female follow the male and mark right on top of where he marked like it's a game of one up manship. When you see her do it tell her sternly no mark! It's how I handle my male whether he's marking or humping. Your other dog must be submissive by nature and there's no way to change that. Your pup is just trying to set the ground rules.
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Tami |