Sheik Amir Ali (36), a resident of Nelagonda in AndhraPradesh, was arrested in Hyderabad last night, officials said.
Police were on his trail for the last sixteen years.
The intention behind the blast was to create rift between communities, officials said.
The serial explosions that rocked churches in J J Nagar and Magadi Road in Bengaluru, Keshwapur in Hubli and Wadi in Kalaburagi district, had created panic among people.
The outfit was also accused of involvement in similar blast cases in Andhra Pradesh and Goa.