James Michael Wells of Kodiak is accused in a federal murder complaint of killing Petty Officer 1st Class James Hopkins and retired Chief Boatswain's Mate Richard Belisle on April 12.
Another Coast Guard member found the victims shortly after the two would have arrived for work at the station, which monitors radio traffic from ships and planes. Their bodies were found in the rigger building, where antennas are repaired.
The Kodiak Island Coast Guard base is home to cutters, helicopters and rescue swimmers that aid mariners in the Bering Sea and Pacific Ocean.
FBI agents immediately flew to Kodiak Island from Anchorage, about 250 miles away, to investigate the case as a double homicide.
Few details were released in the weeks after the deaths, although FBI spokesman Eric Gonzalez in Anchorage said shortly after the murders that there was "no credible evidence" that the community was in danger. He also said there was no indication the homicides were related to terrorism.
Wells' arrest came after "an extensive investigation" led by the FBI and the Coast Guard Investigative Service, with support from the Alaska State Troopers, U.S. Attorney Karen Loeffler said in a statement.
Wells is expected to appear in court next week in Anchorage, Loeffler said.
No one was immediately reachable by phone Friday evening at the U.S. attorney's office to provide additional details.
Hopkins, 41, was an electronics technician from Vergennes, Vt. Belisle, 51, was a former chief petty officer who continued service to the Coast Guard as a civilian employee.
Reached by telephone Friday evening, Gonzalez declined to discuss specifics of the case, saying the complaint and underlying affidavit are under court seal. He said he expected those documents to be unsealed next week.
Gonzalez declined to comment on a possible motive, what led investigators to focus on Wells or whether any other arrests were expected.
"I just can't comment on anything about this case," he said.
In their jobs with the Coast Guard, Belisle and Hopkins were involved with the installation, maintenance, repair and management of electronic equipment.
Approximately 60 enlisted personnel and civilians work at the base's communications station. That's a small fraction of the estimated 4,000 Guardsmen, families and civilian employees at the Kodiak Island base, the service's largest in the nation.
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