The attack was claimed by a man who said he represented a Baluch separatist group, though Reuters had no way to verify the call, which came from an anonymous telephone number. If true, it would be the first attack in the capital carried out by Baluch separatist rebels and a significant escalation of Pakistan's western insurgency.
This conflict has often been overshadowed by the fight against the Taliban to the north.
Baluch rebels usually confine attacks to their own province, although they have bombed gas pipelines in Punjab in recent months.
"We conducted [the bombing] in retaliation for the military operation," said Mureed Baloch, referring to an operation on Monday in which the Pakistani military claimed to have killed 30 Baluch insurgents.
Baloch said he was from the United Baloch Army, which is banned by the Pakistani government for its militant activities.
Wednesday's early morning bomb targeted a throng of traders assembled for fruit auctions.
Severed body parts and bloodstained clothes were scattered throughout the market, located between Islamabad and its twin city of Rawalpindi.
Police said the bomb was hidden in a box of guava fruit.
"Body parts went everywhere and even hit other people on the head," said Shaheen, a market worker who only gave one name.
Bloody sandals lay amid boxes of straw and fruit squashed in the mud.