The Rambam (Issurei Biya 15:29) is mechadesh that a child who does not know who is parents are (a shtuki or asufi) is still permitted to marry a women who might be an ervah to him - e.g. a child who does not know who his father is does not have to worry that the girl he marries is his father's daughter/his sister. The Rambam proves his chiddush from the pasuk "u'mala'ah ha'aretz zimah" - the Torah warns that znus might lead to mamzeirus by a brother marrying a sister when neither knows who their father is. If it was true that anyone of unknown lineage could not marry anyone who might possibly be an ervah to him, there should defacto never be such a chashash of mamzeirus! Only because we do allow people to marry even if their father was unknown is the Torah's warning of "zimah" necessitated.
The Chasam Sofer writes that this is the source of the famous opinion of the Rambam that sefeika d'oraysa l'chumra is only a din derabbanan, but min hatorah we are not required to be machmir on a safek. Despite the safeik that boy X might share the same father as girl Y (where the father of one of them is unknown), we allow them to marry. (I would raise 2 points: (1) I'm not sure why we would not say the heter is based on rov, but in a 50-50 safeik we should be machmir; (2) the assumption of the Chasam Sofer is you need a makor to be makeil on a s'feika d'oraysa - one could easily take the opposite position and assume that the norm should be to be mekeil unless one can provide a makor to be machmir, and with that I have opened a new can of worms).