Previously, experts have distinguished white-beaked dolphins from Risso's dolphins by their whistles.
Hebridean Whale and Dolphin Trust used a technique called passive acoustic monitoring to record the clicks.
Scottish Natural Heritage said click studies could be an additional aid to indentifying the species.
HWDT correctly identified 90% of its encounters with white-beaked dolphins and 100% of Risso's from their clicks.
SNH has also suggested that further research could be done into how clicks might identify different groups of the animals.
An estimated 80% of the European population of white-beaked dolphins are located in the waters off Scotland and north-east England.
SNH said little was known about the distribution of Risso's dolphin in UK waters or about population structure.
It added that it has been proposed that Risso's dolphin were present off the UK coast all year round.
Five newborn Risso's dolphins were spotted off the Isle of Man in September.
The Manx Whale and Dolphin Watch said the sightings highlighted the importance of the island's waters as a breeding area for the species.
Two species of dolphin can be indentified from one another by analysing the clicking sounds they make, new research suggests.