American non-profit science research group SETI Institute said the moon earlier known as P4, which was discovered in the summer of 2011, has been named Kerberos, after the three-headed dog of Greek mythology.
The second one called P5, which was discovered in the summer of 2012, has been named Styx, after the mythological river that separates the world of the living from the realm of the dead, Xinhua reported.
The moons join Pluto's previously known moons Charon, Nix and Hydra.
The SETI Institute said Pluto's moons are all named for characters associated with the underworld of Greek and Roman mythology, according to the International Astronomical Union rules.
The two names were selected based on the results of an unprecedented internet vote that was held during February 2013, with the ballot receiving almost 500,000 votes, including 30,000 write-in suggestions, the institute said.
"I was overwhelmed by the public response to the naming campaign," said Mark Showalter, senior research scientist at the SETI Institute, who led the team of astronomers in the discoveries of Kerberos and Styx.
Kerberos is the Greek form of the name Cerberus, which was ranked second in the voting, and Styx was ranked third, the institute said.
The top vote went to "Vulcan", based on a suggestion from actor William Shatner of TV's "Star Trek", but it was rejected because that name has already been used in astronomy.
The name also happens to be shared by the Roman god of volcanoes but the Roman god is not closely associated with Pluto, it said.