Answer
In the Name of Allah, Most Gracious, Most Merciful.
All praise and thanks are due to Allah, and peace and blessings be upon His Messenger.
In this fatwa:
The two of them must separate. They will not be held accountable in front of Allah for what they did without having knowledge.
Answering your question, Sheikh Mustafa Umar, President of California Islamic University, states:
Thank you for your question.
Firstly, I am very sorry to hear about this situation. It is very rare that someone would not know their own brother or sister, but it can happen.
When a person learns that they have married their own sibling, it can be very stressful and emotionally damaging. I suggest these two get proper help from an expert counselor on how to emotionally digest this situation.
Marriage to a sibling is not allowed in Islam and is also not valid. A man named Uqbah once came to the Prophet Muhammad (peace be upon him) and notified him that he had just learned that his wife was also his sister through breastfeeding. When the man tried to convince the Prophet to let them remain married he responded, “How can you keep her when that lady has said that she has suckled you both of you? So abandon (divorce) her.” (Al-Bukhari and At-Tirmidhi)
If this is the case for a milk-sister, then being married to a real sister is even more detested. The two of them must separate. They will not be held accountable in front of Allah for what they did without having knowledge.
Almighty Allah knows best.