Skomer is already a recognised Marine Nature Reserve
The sea around Skomer Island off the Pembrokeshire coast will be the first marine site in Wales to be protected by new assembly government powers.
It will become a Marine Conservation Zone (MCZ) aimed at preserving important habitats and species and eventually replenishing fish stocks.
Environment minister Jane Davidson intends creating a network of MCZs.
They will offer varying levels of protection from limited to high restriction of maritime activities.
Skomer, famous for its wildlife including guillemots, razorbills and puffins, is already a recognised Marine Nature Reserve.
Ms Davidson said: "Wales has a rich marine environment and people come from all over the world to enjoy our coast and waters.
"Protecting this environment is one of the biggest challenges we face.
"We want our seas to be clean, healthy and biologically diverse.
"They must be managed sensibly and responsibly for the sake of our economic, environmental and cultural wellbeing."
This environment is vitally important to people as well as wildlife
Countryside Council for Wales
She said it was estimated the coast and marine environment supported 92,600 jobs in Wales and contributed £2.5 billion each year to the Welsh economy.
"The UK has made an international commitment to create a coherent network of marine protected areas by 2012," she added.
"Wales is already making a significant contribution to this goal through the number of existing protected sites that we have.
"These new powers to create Marine Conservation Zones will allow us to complete the journey."
The assembly government's MCZ Project Wales will look into and recommend sites for designating as new zones.
Chief executive of the Countryside Council for Wales, Roger Thomas, said: "The marine environment around Wales is rich in biodiversity, supporting a variety of natural habitats.
"This environment is vitally important to people as well as wildlife - providing our food and recreational opportunities.
"We warmly welcome the assembly government's strategy, which recognises the role of marine protected areas in safeguarding marine ecosystems.
"It provides real hope that this precious resource can become more resilient to pressures such as climate change and exploitation into the future."