The Indian fishermen were arrested by the Maritime Security Agency (MSA) while they were fishing in Pakistani waters of the Arabian Sea, said an official at the Docks police station.
"Their (Indian fishermen's) 16 fishing boats have also been seized by the MSA. They were later handed over to police from where they would be produced before the respective courts," he said.
Of the total 88 fishermen, 40 were arrested late Thursday night while another 48 were arrested yesterday.
Pakistan and India regularly arrest fishermen who venture into each other's waters due to poorly marked maritime boundary.
Some of them spend years behind bars before being repatriated.
In the past the two nations have released the fishermen as goodwill gestures.