Ammon Covino, 39, and Christopher Conk, 40, the president and secretary of Idaho Aquarium, were indicted in November by a federal grand jury, KeysNet.com reported.
The indictment on charges that include conspiracy was recently unsealed.
Covino and Conk were arrested in Idaho last week. They appeared before a magistrate there and were ordered to appear in court in Key West on March 15.
The two men allegedly offered to pay fish collectors $1,250 for eagle rays and $650 for lemon sharks to be captured in the Keys and shipped to Idaho. One collector allegedly sent four eagle rays to the aquarium in Boise last year.
In court documents, prosecutors say Covino responded bluntly when he was warned the collector could not get permits for the rays: "Just start doing it.... Who gives a ----."
Another collector allegedly dealt with Conk, sending the aquarium two lemon sharks. Prosecutors said Conk described the permit problem as "no big deal."
The aquarium, housed in a converted warehouse in Boise, is organized as a non-profit educational center.
In a similar case in early February, two aquarium suppliers in the Fort Lauderdale area were charged with selling juvenile nurse sharks without a permit and angelfish bigger than the maximum legal size to a buyer in Michigan.
Covino and Clark face up to five years in prison if they are convicted.