Thirty tiny seahorses have the survival of their species riding on their backs, with a new conservation program entering a crucial stage in Sydney Harbour today.

The program, financed by the Sydney Aquarium Conservation Fund, aims to monitor and boost the number of White's seahorses - a protected species found only in NSW - in areas where their stocks are depleted.

A total of 18 male and 12 females seahorses were transferred from their small tank at Sydney Aquarium to their new home, the Manly Cove swimming net, this morning.

NSW Department of Primary Industries program developer, marine scientist David Harasti, said it was the first time captive-bred seahorses had been tagged for monitoring.

The tag will expand as the six-month-old seahorses, now just five centimetres in length, mature.

The White's seahorse, named after John White, surgeon general of the First Fleet, lives in seagrass and algae beds and can often be found living on the mesh swimming nets around Sydney Harbour.

"The White's seahorse is very territorial and most will stay within a five-metre zone of where they have been placed," Mr Harasti said.

Mr Harasti and a team of divers will measure their length and numbers every two weeks for two years.

"We're hoping between 20-25 per cent survive and go on to reach their average lifespan of three to four years," he said.

"When I attached them to the net they seemed happy to go back to the real world.

"I'll come back in three days to see how they've moved."

Mr Harasti aims to release 100 seahorses next year if the program proves successful.

Seahorse populations and their habitats around the world are under threat from bycatch, habitat destruction and overfishing.

"Anchoring boats can drag up the seagrass beds which they live in, and they are also used in alternative therapies for medicinal purposes," the aquarium's conservation fund program co-ordinator, Claudette Rechtorik, said.

"The seahorse can't swim very quickly and is vulnerable to the behaviour of humans. We endanger them by polluting their habitats."

Up to 25 million seahorses are traded each year, some poached from nets, for use in vinegar and wine, or for private aquariums.

Mr Harasti today also started a new study monitoring the impact on seahorse populations of cleaning the harbour's swimming nets.

"Hopefully we can let local councils know the best way to keep their harbour nets clean without affecting local seahorse populations," he said.

The female seahorse deposits her eggs into the male's pouch for gestation, the only animal to do so.

Male seahorses give birth to up to 100 offspring four times throughout the summer.

AAP