The Great Dark Spot was captured by NASA's Voyager 2 space probe in Neptune's southern hemisphere. The dark, elliptically-shaped spot (with initial dimensions of 13,000 × 6,600 km, or 8,100 × 4,100 mi) of GDS-89 was about the same size as Earth, and was similar in general appearance to Jupiter's Great Red Spot. One major difference compared to Jupiter's Great Red Spot is that Neptune's Great Dark Spot has shown the ability to shift north-south over time, while the Great Red Spot is held in the same latitudinal region by global east-west wind currents.[1] Around the edges of the storm, winds were measured at up to 2,100 kilometers per hour (1,300 mph), the fastest recorded in the Solar System. The Great Dark Spot is thought to be a hole in the methane cloud deck of Neptune. The spot was observed at different times with different sizes and shapes.

The Great Dark Spot generated large white clouds at or just below the tropopause layer similar to high-altitude cirrus clouds found on Earth. Unlike the clouds on Earth, however, which are composed of crystals of water ice, Neptune's cirrus clouds are made up of crystals of frozen methane. These high altitude clouds are located somewhere between 50-100 km (30-60 miles) above the main cloud deck.[2] While cirrus clouds usually form and then disperse within a period of a few hours, the clouds in the Great Dark Spot were still present after 36 hours, or two rotations of the planet.

Neptune's dark spots are thought to occur in the troposphere at lower altitudes than the brighter upper cloud deck features. As they are stable features that can persist for several months, they are thought to be vortex structures.