Amarena was one of the most popular of the Marsican brown bears in the Abruzzo National Park in central Italy, often pictured in and around the area with her offspring.
A local man was immediately identified as the shooter, according to park authorities, which condemned the "very serious incident".
The 56-year-old reportedly told police he fired out of fear when Amarena entered his property on the outskirts of the town of San Benedetto dei Marsi, outside the park area.
Amarena was one of only about 60 such bears in the park, and one of the most prolific females, filmed this summer out and about with her two cubs.
Their fate is unknown, although a search was underway Friday to try to find them.
The park authorities said there was "no reason to justify" the shooting even if Amarena had previously caused damage including to agriculture nearby, as "she never created any problems for humans".
Marco Marsilio, the president of the Abruzzo region, repeated that the bear was no danger and condemned the "incomprehensible" shooting.
The Marsican bear is a subspecies of brown bear that only lives in the central Apennine mountains.
The death of Amarena -- one of a limited number of adult females -- "represents a serious blow to the bear's hopes of survival", environmental campaign group WWF Italia said.
In a statement, it said it would seek to bring a civil action against the shooter, who could also face judicial proceedings.
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