Bonito flakes are difficult to replace in Japanese cuisine. The flavor of bonito flakes is unique and it plays such a major role in Japanese food that omitting it can ruin a dish. That said, bonito flakes are not always easy to find outside of Japan; however, you do have some options if you cannot find it and don’t have any in your kitchen.
Your best bet: Kombu
Sometimes spelled konbu, kombu refers to the edible kelp commonly used to make dashi. Kombu is often used along with bonito flakes in awase dashi but can be used by itself. In fact, it is used alone by many people in Japan who do not eat animal products.
Kombu provides the same benefits that bonito flakes provide, which is that it enhances the umami character of a dish. Kombu is the source of glutamic acid/glutamate, which was isolated to create monosodium glutamate.
Kombu dashi is made by steeping dried seaweed in water without boiling it; you heat the water and then turn the flame off just before the water starts to boil. The resulting dashi may be used as the basis for many Japanese dishes including miso soup and ramen. Dashi made with kombu won’t have the slightly fishy flavor of one made with bonito flakes but it will still enhance the savory flavors in a dish.
The dried kombu leaves are a good substitute for bonito flakes in other applications as well. You can roast and grind them for use as a topping on noodles, tofu, and vegetables.
A decent second choice: Shiitake mushrooms
Dried shiitake mushrooms are another great source of umami flavor. Along with kombu, shiitake mushrooms are commonly used to make vegetarian dashi. The dashi consists of the water used to rehydrate the mushrooms. Shiitake mushroom dashi is not widely used in traditional Japanese cooking because of how intense its flavor profile is; the flavors used in classic Japanese cuisine are restrained and shiitake dashi can overpower them. However, it can work in some dishes and may be better suited for a Western palate.
Shiitake mushrooms have the benefit of being easier to find in Western grocery stores when compared to other substitutes for bonito flakes. If you can’t find dried shiitake mushrooms you might be able to find fresh ones in the produce section and dry them yourself with a food dehydrator.
In a pinch: Iriko
Iriko are baby anchovies that are commonly sold in Asian stores and which are a popular main ingredient for dashi. They are sometimes called niboshi as well. Iriko can range between 1.5 inches and 3 inches long with the larger ones being more flavorful and giving a more intense umami flavor to food. You can use dashi made with iriko to flavor all of the same dishes that require bonito flake dashi. For example, iriko dashi is a common alternative to bonito flake dashi for making miso soup and udon noodle soup. It also complements the flavor of a kombu dashi very well.
Nutritional yeast is not a traditional Japanese condiment nor is it commonly used to make dashi; however, it does provide a strong umami flavor. You can use it as a topping for tofu, noodles and other savory dishes that you would otherwise top with bonito flakes.