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In the beginning of the anime we're lead to believe that Daikichi's grandfather and this Masako woman are Rin's parents.

During the anime they confirm that Masako is Rin's mother, but they leave the father's identity up in the air. If Daikichi's grandfather was Rin's father, he would have had to taken part in her conception at 73 years old - not impossible, but it's still a stretch.

Is Daikichi's grandfather really Rin's father? Is this revealed in the manga?

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Manga spoilers ahead:

In chapter 40 of the manga, Rin requests her family register from city hall to learn about her mother. Daikichi intercepts the response letter and after confronting Rin about it, agrees to schedule a meeting with her mother. Meeting her, Rin learns that her mother was the housekeeper at Souichi's place. In chapter 54 Rin's mother reveals, that Rin is not Souichi's daughter (he just adopted her). Daikichi already knew this after reading the will of Souichi while Rin was still a child.

More spoilers about the implications of this and ending of the manga, not directly answering the question. You probably don't want to know if you liked the pure ending of the anime:

Rin told her mother that she likes Daikichi. This is what triggered the mother's response about Souichi not being the father. Upon learning that Rin shares no blood ties with Daikichi, she decides to marry him. Which he accepts to after asking her to at least wait for her graduation (2 years later).

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    Does the manga ever identify who the father actually is? Or are we just supposed to assume it's some random guy that Masako had sex with?
    – senshin
    Feb 16 '15 at 20:03
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    @senshin I didn't put that in because I read this some time ago, and might have forgotten, but I don't believe we ever get to know him. It is certainly not the guy who is the father of Masako's second child (she explicitly says that).
    – mivilar
    Feb 16 '15 at 20:39
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After watching the Series, I believe so, as no other figure appears, nor is mentioned. I think it is safe to assume this is the case, as no other information is available.

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