US Central Command said in a statement that five other service members aboard the aircraft had been rescued after the crash, which took place about 32 km off the southern coast of Yemen at 7 pm (16000 GMT).
A US official told Reuters that the cause of the crash was under investigation.
"When the incident took place the helicopter was not very high above the water," CENTCOM spokesman Colonel John Thomas said.
The United States has been carrying out air strikes against al Qaeda in Yemen, with at least 80 launched since the end of February.
A small number of ground raids using US Special Operations forces have also taken place, including one in January which resulted in the death of a US Navy Seal.
The US Coast Guard recently said that it had suspended its search off Hawaii for five Army aviators missing since their Black Hawk helicopter crashed earlier this month.
In April, a Black Hawk US Army helicopter crashed on a Maryland golf course, killing one crewmember and seriously injuring two others.
Last month, a military transport plane crash killed 16 service members including elite special operations forces in northern Mississippi.