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The penis is translated as "阴茎" (literally "yin stem"), but it is a male organ. In the traditional concepts of yin and yang, "阴" is generally associated with the female sex.
To support the idea, the term "阳具" (literally "yang tool") is also used to describe the penis (and scrotum).
Why is the penis, a male reproductive organ, associated with the word "阴"?
According to this fengshui expert, the penis and the vagina are both named not because of the gender of the bearer, but via Western medical terminology because they originate from the perineum (会阴).
“阴茎”这个称呼不是中国人发明的。它属于从西方医学中翻译过来的外来语，与我们中国的阴阳学说无关。从解剖学角度来讲，耻骨至肛门之前的区域叫会阴区。在这个区域的内在“通道”称作“阴道”，外在如茎之物称作“阴茎”，想一想也是很形象的。而以阴阳学说为基础的中国古典医学并不把男性生殖器叫阴茎，而是称为阳根、阳具或者阳物。
The answer by Chinese boy is right, 陰 is a technical term for the genitals, male or female.
Etymologically, 陰 as genitals may very well have come from dark, hidden, etc. as Colin suggested above. Morohashi's Dai kanwa jiten cites 釋名, a late Han dynasty dictionary, for this meaning: 陰，蔭也。言所在蔭翳也。 Not so different from English 'privates' perhaps.
Examples of 陰 without regard to male or female include 陰部 'genitals', 外陰 'external genitalia', 陰毛 'pubic hair', 陰蝨 'crabs' and so on. Other male body parts using 陰 include 陰囊 'scrotum'.
或者说在传统的观念里，头为阳，越往下即为阴。凑字数凑字数，凑字数。
阴是医学叫法，指的是平时遮住的地方。阳是传统叫法。
因为生殖器官所在的位置叫下阴，生殖器官中的“阴”和男女的“阴阳”是不能作对比的。
