This year's awards marked the 100th anniversary of US journalism's top honours which began in 1917 after a bequest from newspaper publisher Joseph Pulitzer.
The AP's prize-winning Seafood from Slaves report was an investigation into the mistreatment of workers in South-East Asia used to supply seafood to international supermarkets and restaurants.
The reporters "found captive slaves, countering industry claims that the problems had been solved", AP executive editor Kathleen Carroll wrote in her nomination letter to the Pulitzer judges.
"US customs records show the (slave-peeled) shrimp made its way into the supply chains of major US food stores and retailers such as Wal-Mart, Kroger, Whole Foods, Dollar General and Petco, along with restaurants such as Red Lobster and Olive Garden," the AP reported in the series of 10 articles.
Major Australian supermarkets were also implicated in the report.
Coles, Woolworths and Aldi supermarkets confirmed in December they sourced seafood from the giant company Thai Union that received its prawn supplies from companies accused of slave-like conditions, including bonded and child labour.
The coverage resulted in the freeing of 2000 slave labourers and sweeping reforms, the Pulitzer board said.
It comes just days after a damning report by Greenpeace into the labour abuses allegedly conducted by Taiwan's vast distant water fleet that indentures 160,000 migrant workers.
Migrant crisis and shootings coverage honoured
Reuters and The New York Times shared the breaking news photography award for images of the European refugee crisis.
The Reuters photo coverage was led from Greece by Yannis Behrakis, chief photographer for Greece and Cyprus.
"We showed the world what was going on, and the world cared. It showed that humanity is still alive," Behrakis said.
Some showed families rushing ashore, flailing away in the water or collapsing on the beach. Others juxtaposed the rafters at sea with a cruise ship or a leaping dolphin or the setting sun.
The Pulitzer Board, in conferring the most prestigious honours in US journalism and the arts on Monday, also honoured the Los Angeles Times for breaking news reporting for its coverage of the massacre by Islamist militants in San Bernardino, California.
The prize for national reporting went to the staff of the Washington Post for developing a database on fatal police shootings and those likely to fall victim.
Alissa J Rubin of The New York Times won in the international reporting category for her stories on the inhumane treatment of Afghan women.
Viet Thanh Nguyen won the fiction award for The Sympathizer, an immigrant story about a "man of two minds" and two countries, Vietnam and the United States.
(Fishermen from Myanmar and Thailand ready for repatriation by Indonesia's illegal fishing taskforce. AFP: Ugeng Nugroho/Indonesia government handout)