Malik's biological father is the true parent of Malik Vaccaria. For reasons unknown, Elizabeta told Malik that the Count was his father.
However, the belief is, Elizabeta did so in order to have him inherit the title of Count Dracula. Malik would believe it was his right as the eldest son. He would go along with Elizabeta's plan to assassinate his rival-in-power Vladimir Dracula (the younger son), then claim the title for his own. Elizabeta would become his second-in-command and they could wreak havoc on the remaining Dracula members, as revenge for Elizabeta's banishment 300 years ago (to see more, check here).
Following it being revealed that the Count was not actually Malik's father, several theories have emerged of who his dad actually was. These theories are:
◾ Arta Dracula: There is some speculation about whether or not Elizabeta's actual husband was Malik's real father.
Evidence for: He was Elizabeta's actual husband, and as such was in a position where he could of easily gotten her pregnant.
Evidence against: If this was the case then Malik would still have been a Dracula, and thus able to enter the bloodmirror, which he was not.
◾ "Agabeta": Not much known about him, but another possible theory.
Evidence for: His name was on the family tree.
Evidence against: It is unlikely that Elizabeta would allow the name of Malik's actual father to be recorded on the family tree, as that meant is it was even looked at her whole plan would be ruined. However, as his supposed age would be around that of the Count's, there is a possibility that this is actually the Count's real name.
◾ A breather: A not so uncommon theory about who Malik's father may be.
Evidence for: Elizabeta was voery against revealing the name of Malik's father. If he was a breather, this would be a possible explanation why, as having a child with a breather is not only illegal, but would also be humiliating if made public. It would also be another possible explanation as to why he was weaker than even the much younger Dracula's.
Evidence against: Malik seemed very convinced that he was a pure vampire.
Evidence for: Bertrand was very knowledgeable about shapeshifters, which could be seen as a sign he'd encountered one before. The name Vaccaria itself even seemed to also ring bells once he'd heard it after a while.
This also serves to give several possible explanations as well, such as a reason why she seemed semi-obsessed with getting Bertrand dusted, and as to why Elizabeta did not reveal the identity of Malik's father when asked. Since she was trying to convince Malik to free her at the time, it likely would not have done her many favors had she revealed that she's orchestrated the death of his real dad. Especially so as, in his less guarded moments, Malik did seem to badly want a real family.
Evidence against: Bertrand was French and Elizabeta Romanian, unless they both travelled to the same place at some point it would've been very hard for the two of them to encounter each other.
It's, unfortunately, unlikely whether that we'll ever get a definite answer, but if anyone has anymore evidence for/against any existing theories, or even completely new ones, please do add them!