Two motorcycle-borne youths opened fire at the trader in Kachugaon under Gossaigaon sub-division of the district this afternoon.
The trader identified as Birendra Bhakat, was taken to a local hospital in critical condition.
A massive search operation has been launched in the area to nab the miscreants who managed to escape.
Kokrajhar which falls under Bodoland Territorial Administered Districts (BTAD) had witnessed widespread violence between Bodos and minority migrants since July last in which more than hundred people had lost their lives, sources added.