Investigators said while the 53 suspects are charged with drug dealing and gun running, they believe their drug crews are behind at least 20 unsolved murders and more than 40 shootings in recent years.
"For too long, these narcotics rings have operated as virtual drug monopolies in the Bronx," said U.S attorney Preet Bharara at a press conference with NYPD, ATF and DEA officials. "Today we have put them out of business."
Residents knew the gangs by their nicknames like the "Get Money Crew", "Bronx Gun Slingers" and "God's Favorite Children."
Suspects are accused of dealing heroin and crack cocaine and are charged with various drug conspiracy and distribution counts. Investigators said some of the heroin sold in ten dollar bags were dubbed "American Gangster", "Magic" and "Poison."
Investigators said they recovered nine weapons during the course of the investigation at the Jackson and Melrose Projects along Cortland and Park Avenues in the Bronx.
More than 450 agents and police officers searched 22 locations during the raids dubbed "Operation Rotten Apple."
See a full list of names and charges here.
Investigators noted that the three gangs at times battled for turf. Leaders had set up "The Commission" where suspected leaders would meet to help run the drug operations. Police said leaders include Tyrone "T-Mac" Barnes, Dwayne Henry, and Johnny Weaver.
The suspects appeared late Wednesday in Federal Court in Manhattan.
As part of the investigation, officials said they made more than 80 undercover drug buys. And some of the suspects arrested have numerous past arrests for drug dealing and other crimes.
"One of our goals in crushing its operations inside public housing was to improve the lives and personal safety of its law abiding residents," NYPD commissioner Ray Kelly said.