Indigenous plants are, by definition, those native to the locale in question. They are sometimes allowed to co-exist with lawn grass, exotic ground covers or garden vegetation, especially if they are not aggressive growers. Indeed, some homeowners favor them, growing native specimens in their landscapes either as a matter of principle or for practical reasons (for example, they may be drought-resistant plants) -- or both.
For example, some people will include indigenous plants in a woodland garden. And because some types of wildflowers grow under the forest canopy in their natural habitats, they can be fitting candidates for shade gardens in your landscaping. Examples of indigenous plants for eastern North America that can be used in shade gardens include:
Note, however, that not all "wildflowers" commonly seen in a region are indigenous plants for that area, simply because they grow wild there. For example, while there is a type of lupine that is indigenous to New England (United States), the showiest type of lupine that grows wild there is not a native, but rather has been naturalized. Many wildflowers in your area may have been introduced from far-away lands; some may even be invasive.
Another example: Although indigenous to Europe, yellow dock has become naturalized in many other parts of the world.