Actually, I think you want grep():

  @fookeys = grep $HoH{$_}{foo} eq 'bar2', keys %HoH;
  print "@fookeys\n";  # Only `2' is there.
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By the way, your usage of sort() is wrong. The comparison function used by sort() must involve both $a and $b, else sort() cannot do its job properly.

Also, you should realize that sort() will return a copy of _all_ the elements you ask it to sort; that's why you want grep().