The work of Paignton Zoo and Living Coasts in Torquay, all part of the Whitley Wildlife Conservation Trust, was recognised at the 2009 British and Irish Association of Zoos and Aquariums awards, with a Paignton scientist taking a personal accolade.
The zoo won the research project for a study into gorilla behaviour by researcher Kirsten Pullen for a doctorate thesis.
Dr Pullen said: "It is very nice to receive recognition for all the hard work.
"This award is especially important as it comes from the zoo community and was judged by my peers.
"My PhD is a milestone in my career. I aim to do post-doctorate research in this field.
"The work has practical applications for animal husbandry and conservation breeding.
"The award is also recognition for the commitment of both Paignton Zoo and the Whitley Wildlife Conservation Trust to science and research."
Dr Pullen was a zoo keeper and rose to a senior level at Bristol Zoo before joining Paignton Zoo and moving into research.
Paignton also received a commendation in the education section for its junior zoo vet experience and new enclosure category for the £1.5million Crocodile Swamp, while Living Coasts was commended for Mangrove: Roots of the Sea.
The zoo received a commendation in the PR category for its video coverage of the birth of four rare Sumatran tiger cubs in February.
Living Coasts took a marketing commendation for its marketing through the use of an innovative penguin game.
Director of marketing Pippa Craddock said: "We are very proud of our success this year.
"The wins are tribute to our dedication to conservation and the importance of the visitor experience, and to our staff who make our zoos such special places."
Dr Miranda Stevenson, association director, said: "This award demonstrates how much time and effort our leading zoos are investing to help change public behaviour and ensure the future of planet Earth."
The ceremony was held at Knowsley Hall in Merseyside.
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