What is so confusing? If it is the last name of Indira, then it was because she changed it from Nehru to Gandhi because she wanted to marry a Muslim, Feroz (who also changed his last name to Gandhi). Indira was a Hindu. Please read more about it in the comment below:
Her mother was Kamala Nehru as others have mentioned.
Edit based on your comment to anonymous's answer "It is said that nehru multiple illegal relations!! So asked??"
It is easier to hide someone's father but very hard to hide someone's mother. So, I think you can be certain that Kamala was indeed her mother.