Androgynous can apply to both men and women and simply refers to possessing physical traits associated with both sexes (not usually in terms of genitals, but rather facial features and build).
Androgyny refers to two concepts. The first is the mixing of masculine and feminine characteristics, be it for example in the loud fashion statements of musicians like David Bowie as Ziggy Stardust or the balance of "anima" and "animus" in Jungian psychoanalytic theory. Secondly, it describes something that is neither masculine nor feminine, for example the Hijras of India who are often described as "neither man nor woman".
This can also apply to characters whose gender is canonically unknown, or for an original character if it is difficult to tell which gender they are.