The long list of arayos – forbidden sexual relationships – is fairly repetitive because almost all of them are prohibited due to incest. When it comes to the sister of one’s father, we are given another insight. The verse continues, “…(because) she is your father’s flesh.” So, aside from the extra fence the Torah places around the possibility of incest due to the closeness of relatives and the increased possibility of birth defects due to inbreeding, “father’s sister” has an added aspect: it’s an affront to one’s father!
This law applies whether it’s a father’s whole sister or a half-sister on either side, born in wedlock or out of wedlock, from a permitted or a forbidden relationship. However, unlike direct ancestors or descendants, there are no secondary relationships. So, for example, let’s say your father has a sister with the same mother but different fathers. If that aunt has another sister on her father’s side, that woman is not your father’s sister or your aunt. One would be permitted to marry such a person.
This mitzvah applies in all times and places. It is discussed in the Talmud in tractates of Yevamos (54b) and Kerisos (2b). It is codified in the Shulchan Aruch in Even Ha’Ezer 15. This prohibition is #340 of the 365 negative mitzvos in the Rambam’s Sefer HaMitzvos and #129 of the 194 negative mitzvos that can be fulfilled today as listed in the Chofetz Chaim’s Sefer HaMitzvos HaKatzar.