Fergus' parentage is not known.

There is reason to believe he has Irish ancestry, and some genetic studies show that the clan could be descended from Uí Néill, with Y-DNA Haplogroup R1b1b2e, formerly R1b1c7 also identified as R-M222:

http://en.wikipedia.org/wiki/Niall_of_the_Nine_Hostages

http://en.wikipedia.org/wiki/U%C3%AD_N%C3%A9ill_descendants

The Wikipedia article on Fergus says:

Origins of Fergus

Fergus of Galloway first appears in the historical sources in 1136. His origins and his parentage, however, are something of a mystery. Over the years, Fergus’ origins have been the subject of much discussion and even more fanciful fictional elaboration by historical writers.

One theory is that Fergus was descended from a great pedigree of Gall-Gaidhel kings, who might have been known as Clann Dubgaill, claiming descent from a certain Dubgall. Adding believability to this view is the fact that the chief branch of descendants of Somairle mac Gilla Brigte took the name MacDougall, while the cognate name MacDouall was popular in Galloway. However, since the Argyll name comes only from after Fergus' time, this theory cannot be accepted.

A similar theory traces Fergus from a certain man called "Gilli," a Gall-Gaidhel "Jarl" of the Western Isles. The reasoning in this case is that the Roman de Fergus, an early 13th century French language Arthurian romance, names its eponymous hero's father as Soumilloit (Somairle). The argument is that the latter was descended from the Jarl Gilli, and therefore that both Somairles had Jarl Gilli as a common ancestor. Likewise, yet another theory identifies Fergus' father with the obscure Sumarlidi Hauldr, a character in the Orkneyinga Saga.

Writers in the late 19th and early 20th centuries had advanced the idea that Fergus was the childhood companion of David I at the Anglo-Norman court of King Henry I of England. This idea was given credence by his marriage to the daughter of King Henry I, his good relationship with David, and his friendliness towards Anglo-Norman culture.

In reality such a relationship is pure fiction. Fergus was almost certainly a native Galwegian. The Roman de Fergus may not be entitled to general reliability in matters of historical correctness, but Soumilloit is unlikely to have been totally made up. Moreover, Somairle (anglicized either as Somerled or Sorley) is a thoroughly Gall-Gaidhel name, and makes perfect sense in the context. In light of the absence of other evidence, we have to accept that Fergus' father probably bore the name Somairle. Other than that, we simply cannot say anything about Fergus' origins for sure.