In a 5- to 6-quart pan over high heat, stir onion in oil until limp, about 3 minutes. Add clam juice, wine, and 2 cups water. Bring to a boil. Add clams, garlic, and pepper.
Cover and cook until clams pop open, 5 to 10 minutes. Sprinkle with cilantro.
Distribute bread cubes equally among wide soup bowls. Spoon clams and broth into bowls.