Jupiter's red spot is actually a giant storm, similar to hurricanes on Earth, but much, much larger. The storm is actually over twice the size of Earth! Why is the spot red? Some scientists suggest that it is because of certain phosphorous containing compounds in the gases that comprise the storm, but the spot's color is not well understood.

Jupiter’s red spot is a storm, probably similar (but much larger) than a hurricane on Earth. How it formed, and why it's still there after over 300 years, we don't yet know. Saturn and Neptune have similar storms, so it's a common thing for gas giant planets to have such storms.