The "Carolina hammerhead," named after the region where it was found, reaches 11 feet long and has been identified cruising the waters at Bull's Bay north of Charleston, St Helena Sound near Beaufort and in the Charleston harbour.
However, biologists suspect these hammerhead sharks occur worldwide, since evidence of them has been found in the past from Brazil to the Indian Ocean.
The number of Carolina hammerheads is thought to be small, 'The State' reported.
"It is a distinct species," said William Driggers, a marine scientist with the National Oceanic and Atmospheric Administration's (NOAA) fisheries division.
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He said it is almost impossible to tell the difference between a Carolina hammerhead and the well-known scalloped hammerhead - except for one major distinction: the newly identified species has fewer vertebrae than its shark cousins.
According to researchers, Carolina hammerheads have 83 to 91 vertebrae, while scalloped species have 92 to 99 vertebrae.
While the difference between scalloped and Carolina hammerheads is subtle, NOAA officials say it's significant to conservation of the species.
Scalloped hammerhead numbers are dwindling in some areas, so Carolina hammerhead numbers would be even fewer, they said.
Researchers concluded recently that the Carolina hammerhead is separate from the scalloped hammerhead.
As many as 56 sharks used to identify the Carolina hammerhead were all collected off the South Carolina coast.