Crinan Hotel proprietor Frances Ryan contacted the Advertiser to tell the story.
'It was overnight on Friday January 31 that someone took down our Union flag which flew at the hotel and replaced it with the flag of Madagascar, and at half mast as well,' explained Frances.
The Union flag was thrown into the sea.
'It was very strange and I wonder where they got the Madagascar flag.
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There is an obvious link to the African island through Frances' son-in-law Jamie Spencer, who founded aid charity Feedback Madagascar, but Frances said he knew nothing about it.
'If it's a protest, it's a strange one because we are fans of the EU, the UK and, of course, Scotland,' said Frances, 'and we have staff from many different EU countries.'
She revealed one tantalising clue, however.
'Whoever tied the rope to the flag knew how to tie proper knots, so there might be a nautical connection,' said Frances.
The hotel's flag was recovered and restored to its former position after being washed up on the Crinan slipway the day after it was removed.
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