"The Secretary has reluctantly accepted his decision and wished him well", State Department spokesperson Heather Nauert said in a statement provided to HuffPost.
In his current post, which he assumed in October 2016, Yun served as the chief USA delegate to long-stalled six-party talks on Pyongyang's nuclear program and coordinated with Japan and South Korea on North Korea policy.
Some argue that Yun's retirement reflects pent-up frustration in American diplomatic circles as the State Department loses influence under the current administration.
Envoy on North Korea retiring
Yun traveled to North Korea last year to retrieve Otto Warmbier, the American student who had been detained for over a year.
Former deputy assistant secretary of defense for East Asia Abraham Denmark called Yun's departure "a huge loss for the US government at a critical moment".
Yun, like Tillerson, is said to favor dialogue with Pyongyang - a tricky position to take in a Trump administration focused on pressure rather than engagement. -North Korea dialogue, according to the ministry.
-North Korea talks before joint military exercises between the USA and South Korea resume in April, Kang said that anything is possible but it's hard to say now that the talks will be held.
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Kang Kyung-wha, foreign minister of the Republic of Korea, also called for the resumption of visits between separated Korean families, as a "humanitarian and human rights issue", especially are many are in their 80s.
South Korean President Moon Jae-in has worked to break this impasse, holding talks this week with top North Korean representatives, including Kim Jong Chol, who is accused by Seoul of being behind the sinking of a South Korean warship in 2010 that killed 46 sailors.
"The North Koreans have always said they would be happy to talk to the United States, and in fact they are eager to come and talk to us - as one nuclear weapons state to another", said Ralph Cossa, president of the Pacific Forum at the Center for Strategic and International Studies.
"Joe Yun is the only senior official left at State who has experience dealing with the complexities of North Korea policy".
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His last day at the State Department is Friday.
Washington and Pyongyang have been at loggerheads over the denuclearization issue, with the USA saying any talks must be centered on that and North Korea vowing never to give up its "treasured nuclear sword". With Yun's departure, the biggest fear is the end of using diplomacy with Pyongyang.
US-North Korea relations became increasingly fraught in 2017 when Pyongyang tested long-range missiles it said could reach the US mainland and Washington spearheaded punitive sanctions against the Kim Jong Un regime. "And if it does, we are ready to work together towards a brighter and prosperous future for North Korea", Kang told the Geneva forum. High seas petroleum transfers to North Korean vessels are prohibited under U.N. Security Council economic sanctions on Pyongyang's nuclear program.
He warned if the latest sanctions do not work, "we will have to go to phase two".
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