The primary difference between these two types of seasonings is the peppers used. Chili flakes are made from a single type of pepper, while red pepper flakes can be made from a wider variety of dried peppers, including bell peppers and cayenne peppers. As a result, chili flakes tend to be milder than red pepper flakes. In terms of flavor, chili flakes have a fruitier taste, while red pepper flakes are more intense.