I would say with . The girl with a ponytail. we use in mostly for clothes.
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MataputihThe girl WITH a ponytail
The girl IN a ponytail
WITH is the normal way. The same idea as "The girl WITH the ipod". The pony tail is something she has WITH her (even though technically it's PART OF her).
For "Girl IN something", IN means INSIDE. This may mean that the girl is INSIDE some item of clothing, or INSIDE some other type of thing. You ma