Some salty dogs may think that this nautical adjective pronounced 'hên-kee-'do-ree has something to do with a dory – a good small boat. It was surprising to discover that the expression may have nothing to do with any kind of sea vessel. Many resources tell the tale about it arising from the name of a street in the Yokohama, Japan; a waterfront district where sailors on leave could find were bazaars and other entertainments, anything his heart desired. The yarn does make sense because dori is the Japanese word for a road, in particular a broad or important one.
    It is said that Honcho-dori was the Times Square of Yokohama, and thus a favorite hangout of U.S. sailors on shore leave. So popular did this street become among sailors, it is said, that "Honcho-dori" entered naval slang as "hunky-dory," a synonym for "Easy Street," or a state of well-being and comfort.
Nowadays the expression describes something that is ‘excellent, enjoyable, pleasant or A-OK’ and in all probability hunky-dory is a modification of hunky meaning safe or all right. This comes from the Dutch word for goal, honk or “home” in a Frisian variation of the game of tag. The pastime reportedly arrived with the Dutch in New Amsterdam; later New York and is related to another reduplicated term; hunkum-bunkum. To pull off "hunk" or "hunky" in this version of that childhood game was to make it "home" and win the game. To achieve "hunk" or "hunky" in a child's game was to make it "home" and win the game and so "hunky" already meant "O.K."

Another plausible story related to this crackerjack colloquialism is that soon after Commodore Perry's famous trip to Japan in 1853 the term appeared in American everyday speech and by 1877 this marvelous little tale was being cited in Bartlett’s. Others are more skeptical of this history saying the birth of the phrase is really anonymous:

    Hunky meaning fine or splendid dates to 1861. The adjective hunk meaning safe or secure is even older, dating to the early 1840s. Given these earlier usages predate Perry's opening of Japan, it is unlikely the word derives from a Japanese source. In short, it's another one of those that we must mark "origin unknown.”
The Morris Dictionary of Word and Phrase Origins has a similar etymology about the Japanese street and the Dutch word meaning "goal." Save for one small detail that "hunky-dory" was first used during the American Civil War, quite some time before American sailors became frequent visitors to Yokohama. This other explanation holds that the whole hunky-dory thing began with a song by the Christy Minstrels during the Civil War. With the title 'Josephus Orange Blossom', it has a line about 'red-hot hunky-dory contraband.' The song was a huge hit and hunky-dory became part of the trendy slang of the period. Because Japan was not opened to foreign ships until after Commodore Perry's visit in 1853, some time after the US Civil War from 1861 to 1865; the Yokohama theory becomes uncertain. Still it remains one likelihood and many surmise that since hunky-dory was already an established slang term when American sailors first had shore leave on Huncho-dori Street it fell into place as an indication that everything’s okey-dokey.

Two more examples of the linguistic phenomenon of reduplication for hunky-dory, all used to mean everything’s top notch are hunky-doodle, and hunky-dunky. Some synonyms for this first-rate phrase are first-class, splendid, heaven-sent, lucky, dandy, topnotch spiffy and copacetic. Some British might identify tickety-boo as meaning the same thing. The Random House Historical Dictionary of American Slang advocates one more narrative about a popular variety performer named Japanese Tommy who could have established the term in America about 1865. Others say that what he actually may have done is melded the name of the street in Japan with the American "hunky."

At least two different sources; one is a even in print Morris Dictionary of Word and Phrase Origins, claim the phrase originated during the Civil War "before" Perry's voyage. Spending a lot of time puzzling out the dates of Matthew Perry's arrival in Japan on July 8th 1853 with the text of a proposed commercial and friendship treaty along with his return trip in 1854 asking for humane treatment be extended to sailors shipwrecked in Japanese territory, that the US be allowed to buy coal and that the Japanese ports of Shimodo and more to the point Hakodate be opened to US commerce. When the time line of the two events are compared; Perry's voyages 1853 and 1854 with the American Civil War 1861–1865

Deferring to encyclopedia sources for dates as being the most reliable. The war obviously took place almost a decade after Perry's famous voyage. I would put forth that the evidence suggests a theory that the phrase originated in Japan, then later used in the song lyrics during the war between the North and the South as making the most sense. What seems certain is that hunky-dory was a play on words in all probability obtained from the adjective hunk. It may possibly be that hunky-dory was the result of a bilingual pun, invented because American sailors knew the word dori and prefixed it with hunky as to tell comrades about a Japanese street of earthly delights.

Sources:

Online Etymology Dictionary:
www.geocities.com/etymonline/h4etym.htm

Word Origins: http://www.wordorigins.org/wordorh.htm#Hunky-Dory

World Wide Words:
http://www.quinion.com/words/qa/qa-hun2.htm

yourdictionary.com:
www.yourdictionary.com

xrefer:
www.xrefer.com

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