PORTLAND, Maine — The former longtime manager of one of the state’s largest lobster cooperatives pleaded guilty Thursday afternoon to tax evasion as a result of a lengthy investigation that started nearly two years ago into the reported theft of a huge amount of crustaceans.

The charges and plea by 53-year-old Robert Thompson of St. George are a disappointment to the president of the Spruce Head Fishermen’s Cooperative.

Thompson appeared in U.S. District Court in Portland and waived going through the grand jury process. He instead pleaded guilty to one count of tax evasion and one count of violating the Lacey Act, which prohibits the illegal sale of seafood.

Assistant U.S. Attorney Julia Lipez said after the hearing that the tax evasion offense carries a possible sentence of five years and $250,000 fine while the Lacey Act violation carries up to a year in prison and $100,000 fine.

“Robert pled guilty and will take his licks for skimping on his taxes, but not any more licks than he’s due,” Thompson’s attorney, Walter McKee, said after the hearing.

The U.S. probation office will compile a pre-sentence report, and sentencing is expected in the spring.

Thompson, who had been the manager of the cooperative for 20 years, was initially arrested in October 2012 by the Knox County Sheriff’s Office and accused of stealing a large amount of lobsters. A civil lawsuit later filed by the cooperative alleged that he stole more than $1 million worth of lobsters from members. That lawsuit was later dismissed with terms of the deal not being revealed.

The felony theft charge against Thompson was dropped by the state in May 2013 after the district attorney’s office said it did not want to turn over evidence to the defense because it could jeopardize a federal investigation, which included the IRS Criminal Investigation Unit. The Knox County Sheriff’s Office and the National Oceanic and Atmospheric Administration, Office of Law Enforcement also assisted.

Thursday’s filing was the first public action taken by the federal government against Thompson.

Two months ago, the owner of an Eliot seafood dealership was sentenced to 45 days in jail and fined $100,000 for illegally structuring cash deposits linked to lobsters purchased from members of the cooperative.

The lobsters John Price, 58, acquired from the cooperative involved side sales made by members of the cooperative who were not licensed dealers, according to the federal government.

Price was sentenced in October in U.S. District Court on 12 counts of illegal currency structuring and one violation of the Lacey Act. Price pleaded guilty to those charges in January.

The federal government contended Price structured bank deposits from lobster sales to avoid reaching the $10,000 level that requires filing currency transaction paperwork with the U.S. Treasury Department.

Assistant U.S. Attorney Lipez said two months ago that the U.S. attorney’s office agreed the purchases by Price involved side sales from members of the Spruce Head Fishermen’s Cooperative in South Thomaston.

That acknowledgement contrasted with how the criminal investigation began more than two years ago when Thompson was arrested.

Casey Morrill, president of the cooperative, said Thursday he was disappointed that Thompson was not charged by the federal government with theft.

“We’re happy with the guilty plea by Robert Thompson and glad this is in the past and we can move forward,” Morrill said.

According to a police affidavit filed in court two years ago, the cooperative’s board of directors met in January 2012 to voice their suspicions about Thompson. One board member told police he had spoken to a lobsterman in Harpswell and said the man’s son was a truck driver for the Price seafood dealership who dropped off large amounts of cash to Thompson.

Price’s seafood business was the primary buyer of lobsters from the cooperative, which has about 56 lobstermen as members.

Mckee, however, said Thursday, “Our view was always that there never was a theft case to begin with. The best case the state could make was that Robert was involved in side deals to buy lobsters from co-op members. That wasn’t a crime.”

The cooperative last year did settle a civil lawsuit it filed against Price and his J.P. Shellfish business but did not disclose terms of that settlement. The cooperative also agreed, however, to continue doing business with Price.

Price’s attorney, Daniel Mitchell, said in October that Price never tried to hide the side purchases that were initiated by Thompson for cooperative members. He said Price kept records of those purchases and paid taxes on them.

Price had been buying lobsters from the cooperative for 20 years and made the side purchases in years when the supply of the seafood was low and he wanted to meet the demands of his customers. The attorney said Price also agreed to these side sales so he could maintain his relationship with the cooperative.