In Chapter 17 we discover who Mark's father is when one of the Barry brothers, a doctor, enters the house where Molly is staying and discovers her and Mark. The dialogue that ensues is what tells us who the father is:
Mark stopped abruptly, yanked on her hand, and turned to run. One of the Barry brothers
stepped from the dining room into the kitchen, and another closed the door to the outside and stood behind them. The other three entered the kitchen silently and stared in disbelief at the boy. Finally one of them spoke. “Ben’s?” Molly nodded. Her hand clutched Mark’s in a grip that must have hurt him. He stood close to her and looked at the brothers fearfully. “When?” the brother asked. “Five years ago, in January.”
Therefore we find that Ben is Mark's father. Ben is one of the original group of breeders, selected by the Barry brothers, which included Harvey, Jed, Molly, and Lewis, who think they are well bonded.
In the post-apocalyptic novel Where the Late Birds Sang the character Molly goes through her pregnancy in hiding until she gives birth to her son, Mark. The reason for this is that the laws of this dystopian society,--where contamination has led to a scientific debacle--is that pregnant women (who are, with their designated partners identified as breeders) need to be placed in a form of quarantine by spending their pregnancies in what is known as the breeder's quarters. Molly survived her hiding thanks to the Andrew brothers who would bring wood and provisions until eventually going away, not be seen again.
Ben, a clone of David, is the leader of an expedition to D.C. with Molly and other clones. The main mission is to get supplies that were left over from before the apocalyptic ending of the world.
During that trip, the clones realize for the first time that they are not as bonded as they thought, and they start to separate and fight. It was a terrible time, and the loyalties were put to the test.
Ben, as a leader, was able to keep his mental state together. However, Molly (a clone of Celia), realized that she really did not belong to the group and, as a result, she became an outcast and was sent to live in Sumner House. It is at Summer House when she and Ben reconnect and become lovers. This goes strictly against the rules of the compound so she was forced to hide out.