Marine biologist Professor Ho Ping-ho found two of the creatures while researching the environmental impact of a shipwreck on Kenting National Park.
He said: "One was dead while the other was dying when they were found on a beach of Chialoshui."
They are similar to a species that lives around Hawaii, Polynesia and Mauritius, but the new crabs have clam-shaped shells with white polka dots, which makes them distinct.
Both are female and the biggest measures 2.5cm across.
Although the crabs are now dead, they have been made in to specimens for further study.
Professor Ho's discovery has been confirmed by another specialist. He is now writing an essay on the new species.