While there is no universal standard for salt and pepper shakers, it's common to put pepper into the shaker with bigger holes. This is because pepper is often lighter and less dense than salt, meaning it needs more space to flow smoothly.
The traditional debate over salt and pepper shakers involves the amount of holes. In Europe, the pepper shakers often have more holes. However, salt shakers in the U.S. typically have more holes than pepper shakers. This reflects the value of the different spices. Salt is more common in the U.S., while pepper is valued more in European dishes. Because of the lack of universality in the standards, it may be a good idea to mark the salt and pepper shakers to avoid confusion.