Phillip Feng, 36, and 35-year-old Victor Bae were arraigned on several charges, including criminal and unlawful possession of marijuana and possession of a firearm.
Police say both were seen Wednesday loading a large container into a truck and driving it to an address on Jay Street near Nassau Street.
Authorities say the men were carrying about 350 pounds of marijuana in their truck.
The following day, police say they searched the Jay Street address and seized about 150 pounds of marijuana.
Investigators also found more than 1,000 packed containers of ready-for-sale drugs, including marijuana, mushrooms and liquid PCP.
Police say the drugs hold a street value of about $2.5 million and that the operation made about $10 million a year.
Both men are being held on $2 million bail. Their next court date is March 15.