Don't see genetics being a problem - its pretty common in the animal kingdom to see inbreeding which would make a Cornish hamlet blush. The reason its a problem in humans is our pathetically small gene pool - European humans are believed to have been reduced to no more than 1000 by the last ice age. Which means two randomly selected humans of similar continental background are much more likely to share genetic sequences and hence recessive genetic abnormalities. Make it two family members and the situation gets exponentially worse. Two randomly selected members of almost any other mammal species would be much, much more unlikely to share any recessive abnormalities, and as such their offspring, even of closely related animals, would not express them.
Still, realistically, two individuals repopulating a species is a bit of a stretch, and would probably need at least some artificial insemination from human scientists.