Marine patrol officers discovered the lobsters, marked with a v-shaped notch in their tails or mutilated to remove the notch, during an inspection last year of a boat owned by Ricky Curtis, the state Department of Marine Resources said in a statement.
Maine requires lobstermen to notch the tails of egg-bearing female lobsters before returning them to the ocean as a conservation measure. The lobsters may then reproduce several more times.
"We consider this a very serious crime," Colonel Joseph Fessenden, Marine Patrol chief, said in the statement.
"The illegal taking of any lobsters negatively affects the resource and is a direct theft from those lobstermen who abide by the laws every day that they fish," Fessenden said.
Ricky Curtis, 48, and his son Todd Curtis, 29, entered a not guilty plea through the mail at Knox County District Court in Rockland, Maine, a court clerk said.
They face a fine of more than $190,000 if they are convicted of the crime, the statement from wildlife authorities said.
Their attorney, Philip Cohen, declined to comment on the charges.
(Editing by Barbara Goldberg and Nick Zieminski)