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Cain's wife was one of his sisters. God did not prohibit sexual relations with one's close relative until Leviticus 18:6
Some argue that if Adam and Eve are the father and mother of all humankind, then Cain could not have found his wife. Here is the relevant passage:
Then Cain went away from the presence of the Lord and settled in the land of Nod, east of Eden. Cain knew his wife, and she conceived and bore Enoch. When he built a city, he called the name of the city after the name of his son, Enoch. (Genesis 4:16-17
The argument is that if Cain found a wife in a foreign land, then Adam and Eve must not be the parents of every human.
In Genesis 5:4
The days of Adam after he fathered Seth were 800 years; and he had other sons and daughters.
This means that Adam had daughters, one of whom could have been Cain's wife.
Incest was not prohibited by God until Leviticus 18:6
It is very possible that having sexual relationships with one's close relatives was not dangerous during the early period that Cain lived because the people were so close to Adam that the genetic pool was still extremely pure.
However, as time progressed, and people's genes became more and more polluted because of sin, incest became more and more dangerous. Then, at some point in history, God prohibited incest to protect babies from birth defects due to greater risks with producing children with close relatives.
This means that during the early period before God gave this command against incest, people would have married and produced offspring with close relatives, including siblings.
Cain's wife was his sister, and there was no problem with this likely because of the purity of the gene pool during this early period in time. Therefore, we have no problem in continuing to affirm the Bible's teaching that Adam and Eve are the ancestors of every human being.
Some people have trouble accepting possible explanations to alleged contradictions in the Bible, especially ones that they consider a stretch. For example, Dan Barker, president of the Freedom From Religion Foundation, says this:
I have received numerous replies from Christians who think that these contradictions are either trivial or easily explained. Yet not a single "explanation" has been convincing.
The fact is that there are plausible explanations for every alleged contradiction in the Bible. That there is a plausible explanation for an alleged contradiction does not mean that it is definitely the correct explanation for the alleged contradiction.
However, as long as a possible explanation has been suggested, then it has been objectively demonstrated that there is no necessary contradiction regarding the Bible verses and passages brought up.
When people like Dan Barker say that they don't find a particular explanation for a contradiction "convincing," then that is merely their opinion. A plausible explanation has been suggested that eliminates the necessary alleged contradiction. They simply don't like it, which is not at all a relevant argument against the explanation.
To read more about solutions to Bible contradictions and difficulties, check out Norman Geisler's The Big Book of Bible Difficulties: Clear and Concise Answers from Genesis to Revelation. While we do not agree with some of Geisler's theology, particularly concerning his view of predestination, this book is still an excellent resource. It is thorough and filled with research.
Another book to check out is Tim Chaffey's Demolishing Supposed Bible Contradictions: Exploring Forty Alleged Contraditions, which also answers many alleged contradictions in the Bible.