The Great Dragon Extinction technically was the loss of many great dragons during the Thousand Year Dragon War, but the dragon population continued to suffer for the next several generations of dragons, as many still held grudges even against Dragons of the same color.  Despite such strong grudges, many weren't sure why they were fighting, but because of the losses in their families, they continued their minor quarrels.

 

The dragon population seems to have stabilized again around the time of the Great Exploration.