Hamilton mayor Paula Southgate said the donation was extraordinarily generous, especially given the ongoing uncertainty around Covid-19.
"I'm just incredibly grateful to have people like Craig and Jenny in our city – we all should be. They run a fabulous café and have also been huge supporters of the Hamilton Gardens.
"The gardens are a treasured place for so many people and it's people like Craig and Jenny, who go above and beyond, over and over, who help make this place and our city so special."
She said the donation couldn't have come at a better time as there is a lot of work underway for and in the gardens.
"We have the Egyptian Garden opening early next year and work on the visitor centre is also planned. So, it's all go and I'm looking forward to seeing the changes this donation will fund."
Craig said the donation followed a long family tradition of giving back to the city. "We could think of no better place to contribute than Hamilton Gardens, a place that has become our second home.
"We have seen the pulling power of this stunning place, it attracts thousands of domestic and international tourists to Hamilton. The Gardens have become part of the fabric of our beautiful city.
"They also hold a special place in the hearts of many, including the hundreds and hundreds of members of the Friends of the Gardens."
Community committee chair Mark Bunting said passionate people like the Frasers have helped the Gardens become world-renowned.
"There aren't many people who know and love the Hamilton Gardens like the Frasers. Like the Gardens, they are Hamilton through and through. We're incredibly lucky to have the generosity and dedication of people like Craig and Jenny."
The Frasers also previously donated $10,000 towards the Hamilton Gardens development programme and shared 50 per cent of the costs of the outdoor cafe awning installed last summer.