Homophones are pairs of words (or phrases) that are quite distinct in spelling and meaning but have the same pronunciation. For example:
(In the reference section of this site, you will find an extensive list of homophones.)
A typical homophone clue in a cryptic crossword is this one:
Remained sober, so we hear (6)
You should read this as: a word meaning remained which sounds the same as a word meaning sober. The fact that this is a homophone clue is signalled by the indicator so we hear.
Other common homophone indicators are: heard, so it's said, in speech. And here, for reference, is a more extensive list of homophone indicators.
Here are a few more examples of homophone clues:
Neckwear that's Siamese, so we hear (3)
Narrow channel - not winding, we hear (6)
Expensive animal, by the sound of it (4)
I'd heard and observed (4)
An advance, we hear, on its own (5)
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