The Karner Blue butterfly's habitat is being destroyed. Wooded areas are being turned into agricultural land, forest fires suppressed, shrubs and hardwood trees encouraged to take over their range, and logging and urbanization (development of towns) taking place in their usual habitats. For the Karner Blue to survive, its habitat needs natural disturbances (like wildfires and grazing by large mammals) to set back encroaching forests, which helps wild lupines and nectar plants the tiny butterfly so relies on for food to thrive. Because of the rarity and beauty of this species it is also very desirable for butterfly collections.

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