Cryptic crossword clue
Reproductive organ set man apart 6

The most common and most likely answer to this crossword clue is the 6 letter word STAMEN

I've seen this crossword clue in Financial Times
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Buddy explains!

The straight part
We know that "Reproductive organ" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case reproductive organ = stamen.
The cryptic/wordplay part
In cryptic crossword there's often an wordplay/cryptic part as well.
This part involves a more complex hint, such as an anagram, homophone, hidden word, etc.
Sadly, We don't have an explanation for this specific crossword clue yet.

What does STAMEN mean?

STAMEN noun
  1. In flowering plants, the structure in a flower that produces pollen, typically consisting of an anther and a filament.

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