The two, identified as Mithoo Prasad (45) and Binoy Karmakar(62) were kidnapped from Deku Bazaar last evening, the police said.
An operation has been launched to rescue them, the police said.
Karmakar is a well known supplier of livestock, to the main market in the Garo Hills and is a resident of Nakham Bazaar.
The GNLA has been declared a terrorist outfit by the Centre in January this year.