The Deep has launched Project Penguin, which coincides with the aquarium's plans to open a penguin enclosure early next year.
Heron Foods stores will raise money to protect endangered penguins, as part of its new charity support for The Deep.
Project Penguin is a new scheme, which will raise money to help protect endangered penguins in the wild.
They will be taking up residence in The Kingdom Of Ice, alongside information explaining to visitors about the threats to the penguins' habitat, issues surrounding climate change and ocean acidification.
Fundraising will be carried out in 67 Heron Foods stores, across the whole of Yorkshire and Lincolnshire.
Stores will have collection buckets, penguin cut outs and competitions for customers to enter.
They will also be asking local community groups such as Brownies and Scouts to get involved with bag-packing days to help raise money.
Colin Brown, chief executive at The Deep, said: "We are delighted to have been named as Heron Foods' ' charity of the year and look forward to putting the money raised towards some very worthwhile research and conservation schemes over the coming months.
"The first organisation we are working with is the Galapagos Trust, who will be using the money to help stop the decline of endangered Galapagos penguins. They are one of the most 'at risk' species and face possible extinction.
"This money will be put into projects to further understand their habitats, diet and breeding activity in a bid to help conserve their future."
Mike Igoe, commercial director for Heron Foods, is delighted to be backing the scheme.
He said: "We chose to support the fantastic work done by The Deep as they are committed to making a real difference in conservation and share our desire to raise the profile of Hull and make it a "top ten" city.
"The Deep, like Heron Foods, is an important employer in Hull.
"Our most recent store opening in Hull's Whitefriargate brings the number of Hull stores to 18.
"We are committed to this region and hope our customers will get behind Project Penguin and the fantastic work that The Deep is doing.
"Heron Foods is well known for quality frozen food products and this was a fantastic fit with The Deep's new Antarctic penguin display."