Here is her wedding photo from when she married Jefferson Davis, the man who would later become the President of the Confederacy.
I saw this yesterday, and couldn't believe it. And I showed some colleagues and friends, and they all agree that she looks bi racial.
I've read her wikipedia and done Google searches, but I've found very little scholarship done on this question.
Also interesting is that in official portraits, the painters appeared to have minimized her African American features, such as narrowing her nose, thinning her lips, etc. It appears to be a conscious effort.
It's mind blowing that the first lady of the confederacy was possibly African American.
While the original at NYPL calls this their wedding picture, it's likely not. This is Davis around the time of their wedding - he's clearly much older in the "wedding" shot, looking more the way he did in 1861. At the same time, Varina's dress appears more characteristic of the 1860s than 1845 (round waistline, sheer fabric with a partial lining, bishop sleeves). As other photographs from the 1860s show (ca. 1860 and 1869), her nose was longer and narrower than it appears in that photo (her lips fuller, too). Since this photo is not from their wedding but later, Varina may have been starting to show her age and there may have been some retouching to remove facial wrinkles and shadows, resulting in a broadened nose, the slightly darker skin tone, and the strange flat quality to her face.
I wonder if the photo you have posted has been altered subtly. Here's another version:
http://clevelandcivilwarroundtable.com/images/people/davis/davis_jeff_varina.jpg