The pepper goes in the shaker with the fewer amount of holes. That is the “rule”.

Does salt or pepper go in the 3 hole shaker?

Many people tend to shake a great deal of salt on their food and only sprinkle a little pepper. Therefore, the salt shaker should have more holes in order to improve the flow, while a pepper shaker should do all right with fewer holes.

How many holes are in a pepper shaker?

The salt shaker has two holes, while the pepper shaker has three holes. The holes are pretty large. Be careful when using the salt shaker.