In August, the company's stock fell by nearly a third after it admitted that the documentary "Blackfish" had in fact hurt park attendance.
Branson has been at the center of a media storm surrounding the issue of cetaceans in captivity at marine parks and aquaria. In June, he called together a meeting of marine parks representatives, scientists and conservationists to discuss the issue of cetaceans in tourism.
Many animal welfare advocates were disappointed this month, when the details of the meeting were revealed. Branson and his company, Virgin, had created a pledge for marine parks and aquaria to sign vowing that they would no longer capture whales and dolphins from the wild. But many criticized Virgin for refusing to cut ties with marine parks, arguing that there were "significant loopholes" in the pledge.
Despite Virgin America's move this week, Virgin Holidays continues to offer packages to SeaWorld parks on its website.
Branson is a part owner of Virgin America, though it's unclear if he played a role in the decision to drop SeaWorld this week. The move follows that of Southwest Airlines, which cut ties with the company in July after a 25-year partnership.
Opponents to SeaWorld and marine parks like it argue that orcas in captivity experience severe stress, emotional and psychological problems, and physical ailments in captivity, and that attractions like the "Shamu show" offer little when it comes to conservation education.