The flexibility and evolvability are critical characteristics of modern manufacturing to adapt to changes from products and disturbances in the shop floor. The technologies inspired from biology and nature enable to equip the manufacturing systems with these characteristics. This paper proposes an ant colony inspired autonomous manufacturing system in which the resources on the shop floor are considered as the autonomous entities. Each entity overcomes the disturbance by itself or negotiates with the others. The swarm of cognitive agents with the ant-like pheromone based negotiation mechanism is proposed for controlling the shop floor. The functionality of the developed system is proven on the test bed.