The Reuters photo coverage of Middle Eastern migrants arriving in Europe was led from Greece by Yannis Behrakis, chief photographer for Greece and Cyprus and the Guardian newspaper's 2015 Agency Photographer of the Year.
The team captured a series of images of migrants crowded on flimsy sea craft and their first moments upon reaching Europe.
"We showed the world what was going on, and the world cared. It showed that humanity is still alive," Behrakis said. "We made for these unfortunate people's voice to be heard. Now with a Pulitzer, we feel that our work has been professionally recognized."
Some images 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 Reuters photo staff was named as co-winner for breaking news photography along with Mauricio Lima, Sergey Ponomarev, Tyler Hicks and Daniel Etter of The New York Times, also for their images of the migrant crisis.
It was the third Pulitzer for Reuters, a unit of Thomson Reuters, having won for international reporting in 2014 and for breaking news photography in 2008.
The Tampa Bay Times and the Sarasota Herald-Tribune shared the 2016 prize for investigative reporting. The two Florida newspapers won for collaborative reporting on violence and neglect in the state's mental hospitals.
The Tampa Bay Times took a second Pulitzer, with three of its reporters being honored for showing the consequences of a school board turning some county schools in to "failure factories."
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.
The Boston Globe's prizes were in the feature photography and commentary categories, while The New Yorker took prizes for criticism and feature writing.