Young Male & Ponytail
A: Generally speaking, unless you intend to relocate to a place where no one has ever met you once you have long hair, I think you'll find potential gender-confusion to be less of an issue than you think.
Unless you are striving for an androgynous appearance, the way you dress and your mannerisms will convey your gender clearly. Even the hairstyles commonly worn by guys with long hair are different than those of girls with long hair. Men's hairstyles tend to be simple. The hair is washed, plied with a small amount of product and blown dry or allowed to air dry and styled using the hair's natural wave and style.
Girls, on the other hand, tend to be much more involved. The hair is blown out, curled or straightened and arranged with accessories that are clearly more feminine. There is also the fact that girls tend to develop faster than boys in the pubescent stage, and by comparison, the girls will appear more rounded and filled-out than you will.
The bottom line is that you need to have the courage to wear your hair in any way you desire. There will be plenty of times in the future when you may be required to conform to a specific look (for a job, or by a loved one). Try not to take the issue too seriously. And if you grow your hair long and people start confusing you with being a girl, just get a tee shirt that says "Back off. I'm a Dude."
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See also:
Men's hairstyles
Long hair for men
How men with long hair can fake short hair
Does a man's hair grow faster than a woman's hair?