In a bowl, combine the softened cream cheese, cooked onion and garlic, lump crab meat, grated Parmesan, shredded cheese, dried oregano, black pepper, and chopped chives. Stir until everything is well mixed.
Bake the stuffed mushrooms in the preheated oven for 20 minutes, or until the tops are golden and the mushrooms are tender. Sprinkle additional chopped chives over the baked mushrooms for garnish. Serve warm.