The recent war between Team Aqua and Magma, ended by the heroics of Ruby and Sapphire, is just one chapter in the endless struggle of Kyogre and Groudon for dominance over Hoenn. It is often surmised that Kyogre serves the sea and Groudon the land, but the reality is more multifaceted. Groudon's concept of land is one with many mountains and deserts, and the rest of the land given over to the usage of Man; one with no room for forests in the wilderness. In older eras, Rayquaza, who sought peace and at least had a similar color to the trees, inspired smaller organizations among the peoples of the wilderness: Fortree City is a relic of one such group's effort to live in harmony with the forest and prove both sides wrong. However, this is an exception, for outside of the roads to Fortree and the Petalburg Woods, the trees and the many pokemon they sheltered have spent millennia slowly disappearing.
Treecko have been hit especially hard by this habitat destruction. Their Grovyle parents' usage of Leaf Blade to harvest small trees for food puts them in direct competition with both loggers, who want the trees for themselves, and environmentalists, who fear a recovered population could destroy more trees than the forest could bear, although they only become truly dangerous if they survive to reach the Sceptile stage. Worse, Treecko deprived of their standard diet of trees often attempt to survive by eating wooden homes, and their ability to scale even the tallest of walls leave them all but impervious to traps designed for more common bug-type pests; many settlers have responded by importing predators and shooting them on sight.
It is only through the controversial efforts of Professor Birch's captive breeding program that these strange and ancient pokemon have survived.