Shiitake mushrooms and kombu seaweed are traditional Japanese substitutes for bonito flakes. These ingredients are commonly used to flavor vegetarian versions of broths and sauces that would normally contain dried bonito flakes.
While bonito flakes are most commonly used to flavor stocks and sauces, they have other uses in Japanese cooking as well. They can be sprinkled on food as a condiment or used as a filling in rice balls. Bonito is also sometimes used as a substitution itself, taking the place of more expensive fish such as skipjack tuna. In some countries, bonito is even sold as canned tuna.