There are 4 (four) Pokemon that are confirmed to have been created in ancient times:
Baltoy and Claydol:
Source: http://bulbapedia.bulbagarden.net/wiki/Artificial_Pok%C3%A9mon
Golett and Golurk:
Source: http://bulbapedia.bulbagarden.net/wiki/Artificial_Pok%C3%A9mon
Did the creation...