Manure was used from the beginning of horticulture / agriculture, where it developed: The Neolithic Revolution in the Near East: Transforming

There are more traces left (or discovered) in Europe, they trace back 8,000 years:

• European Neolithic Farmers Used Fertilizers 8,000 Years
• Manure was used by Europe's first farmers 8,000 years ago
• Early Farmers and Manure: Stone Age Europeans Were
• Stone Age Farmers Showed Sophisticated Use of Fertilizers
• Ancestors for the Pigs: Pigs in Prehistory
• History of agriculture - Wikipedia, the free encyclopedia

According to the History of Fertilizer by Dr. James Beaton*:
800-200 BCE Greek writers were writing about the use of manure to adjust the richness of soil for crops.

Theophrastus (Θεόφραστος) (4th-3rd cent. BCE)** was an ancient Greek who wrote two (surviving) botanical texts: Enquiry into Plants and On the Causes of Plants.

In Classical Greece: ancient histories and modern archaeologies (ed. Ian Morris), Theophrastus is cited as writing up some of the earliest lists on the strength of different kinds of manure as fertilizer. The order of strength at this time: human, swine, goat, sheep, ox and pack animals.

* http://www.back-to-basics.net/efu/pdfs/History_of_Fertilizers.pdf
** http://en.wikipedia.org/wiki/Theophrastus