28-year-old Joseph Dougherty and 49-year-old Anthony Merchant will both be facing theft charges when they appear in court.
The crime allegedly occurred over the period of 10 to 12 weeks while Dougherty was warf manager for the company.
State Police started looking in to the matter in November.
According to court documents Dougherty confessed to authorities that he had been involved in stealing the money.
State police say that Dougherty had been writing Mr. Merchant checks as if he was a fisherman for the company, which he was not.
Then Merchant would cash the checks, and the two men would split the money.
According to authorities Dougherty was also writing duplicate paychecks to himself.
Both men were released from the Washington County Jail on $25,000 unsecured bail.