© NASA/Johns Hopkins University Applied Physics Laboratory/Southwest Research Institute
Scientists are at a loss to explain the intriguing spots which are remarkably consistent in both their even spacing along the dwarf planet's equator, and their shape and size.
Each spot appears to be circular and about 480 kilometres in diameter.
"It's a real puzzle-we don't know what the spots are, and we can't wait to find out," says New Horizons principal investigator Dr Alan Stern of the Southwest Research Institute, Boulder, Colorado.
"Also puzzling is the longstanding and dramatic difference in the colours and appearance of Pluto compared to its darker and greyer moon, Charon."
The strange spots were detected in new images of Pluto and its largest moon Charon, taken by New Horizons on June 25 and 27, 2015.
The new pictures, which combined black-and-white images of Pluto and Charon, shows Pluto has two remarkably different faces.
The image on the left shows the side of Pluto that will be seen at highest resolution when New Horizons makes its close approach on July 14.
The hemisphere is dominated by a very dark region extending along the equator, which appears near the bottom of the dwarf planet from New Horizon's point of view.
The image on the right shows the hemisphere of Pluto that faces Charon, with the row of strange spots clearly visible along the equator.
While the origin of the spots is a mystery for now, the answer may be revealed as the spacecraft continues its approach to the Pluto system.
New Horizons has been given a final "all clear" as it speeds ever closer towards its historic once-in-a-lifetime close encounter with Pluto.
After a journey that has lasted more than nine years, the washing machine-sized spacecraft will make its closest approach to Pluto at 21:49:57 AEST, flying just 12,500 kilometres above the dwarf planet's frozen surface.
