During most of the 20th century the market was associated with one or more New York Mafia families. In 1988, the U.S. Attorney's Office filed a suit under federal racketeering laws to appoint a trustee to run the market. A trustee was appointed, but the extent to which he was able to limit organized crime influence was limited.Since 2001, the market has been regulated by the City of New York's Business Integrity Commission in an effort to eliminate organized crime influence.
On November 14, 2005, nearly 4 years after the $85 million structure was completed, the Market opened at its Bronx location. The move had been delayed due to legal problems. The last-minute dispute was between a company which had had a ten-year monopoly on delivering fish from trucks to individual sellers' stalls, versus the cooperative of sellers who wanted to do the task themselves in the new building. When the feuding parties agreed to continue as they had been for another three years, the last obstacle to the move was removed and packing began.
The New Fulton Fish Market Cooperative is the largest consortium of seafood wholesalers in the country, relocated its operations to the Hunts Point Food Distribution Center in the Bronx to an indoor fully refrigerated HAACP facility - The New Fulton Fish Market houses 37 seafood wholesale businesses. These businesses offer the freshest and most diverse selection of seafood combined with competitive pricing and year round availability.