The zoo in the city of Voronezh, some 450 kilometres (280 miles) south of Moscow, was home to species including parrots, eagles, hawks and owls.
But it took the drastic step to put down its remaining 141 birds after 35 died from avian flu earlier this month, local authorities said in a statement carried by Russian news agencies.
The Voronezh zoo itself declined to comment when contacted by AFP on Monday.
A number of European countries have recently taken measures to curb the outbreak of a virulent strain of bird flu sweeping the continent.
The strain of the H5N8 virus has been detected in 17 European countries, according to World Organisation for Animal Health -- including Germany, the Netherlands, Denmark, Poland, Hungary and Sweden.
The H5N1 strain of bird flu has killed more than 420 people, mainly in southeast Asia, since first appearing in 2003.
Another strain of bird flu, H7N9, has claimed more than 200 lives since emerging in 2013, according to World Health Organisation figures.
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