Scientists think the red color is caused by impurities in the planet's atmosphere constantly absorbing ultraviolet and violet light, such as sulfur or phosphorus. The Great Red Spot is quite a mystery.
Nobody is sure how long the storm has been going on.
All we know is that the spot has been visible since the day we first built a telescope strong enough to see Jupiter in the 17th century. Here is a link to pictures of the Great Red Spot taken by Voyager I in 1979. You can learn more about our solar system at our Astronomy channel.