The monarchies two of a handful remaining in Asia have maintained close ties. Bhumibol first visited Japan in 1963, touching off a decades-long friendship with numerous visits back and forth, most recently a visit by Akihito to Thailand in 2006.
Akihito, accompanied by his wife, Empress Michiko, laid wreathes and signed a condolence book at the Grand Palace in Bangkok.
He later met with King Vajiralongkorn
Bodindradebayavarangkun, who ascended the throne after the death of his widely revered father in October.
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Thailand and Japan have traditionally enjoyed close relations, unburdened by the legacy of World War II that has complicated Japan's relations with other Asian countries.
After a brief struggle, Thailand formally became Japan's ally through much of the war, suffering little of the destruction wrought on others like China, Myanmar and the Philippines.
But following a 2014 coup, Thailand's Western allies cut back on assistance, pushing the country's ruling military junta closer to Beijing.
"The visit is symbolic of Japan's interest in boosting Japanese-Thai relations at a time when China seems to enjoy favor in Bangkok," said Paul Chambers, research director at the Institute of Southeast Asian Affairs.
The 83-year-old emperor is Japan's constitutional head of state, a role symbolic rather than political. However, his trips often serve to bolster relations with nations friendly to Tokyo.