EDIT
The Yangtze River, extinction hotspot: The most publicized extinction over the past decade is the baiji, also known as the Yangtze River Dolphin. While the baiji's evolution goes back 20 million years, it couldn't survive China's great development boom. A combination of dams, boat traffic, pollution, overfishing, and electro-fishing led to the species demise giving the baiji the dubious title of the first marine mammal to go extinct since the 1950s. The dolphin was a character in Chinese myths and was colloquially known as the 'Yangtze River Goddess', but none of this could save it from an economic juggernaut.
But the baiji is not alone, another denizen of Yangtze may have vanished recently. A recent survey of the Chinese paddlefish, one of the world's largest freshwater fishes, failed to find even a single individual. While researchers believe the fish probably still survives, no one knows for certain—and no one knows how long it can on in highly degraded habitat. The Chinese paddlefish has been decimated due to the same reasons as the baiji: dams, traffic, and pollution, although overfishing is probably the biggest cause. The last confirmed paddlefish was killed by illegal fishing in 2007. Unless China acts quickly other species of the once fabled Yangtze will not survive the next decade, including the finless porpoise, the Yangtze sturgeon, and the Chinese alligator (although the alligator survives in large numbers in captivity).
EDIT
Big Mammals No More: In addition to the baiji, the decade saw the extinction of two other large mammals. In an ignoble end, the world's last Pyrenean ibex was killed by a fallen tree at the opening of the decade, January 6th, 2000. A subspecies of the Iberian ibex, the Pyrenean ibex once roamed across the Pyrenees in both France and Spain, but spent most of the Twentieth Century on the verge of extinction. Nine years after its extinction, the species returned for a moment: a clone of the subspecies was born—the first clone of an extinct animal—but died from lung failure after a few minutes.
The western black rhinoceros also met its end during this decade. Hunted relentlessly for its horn, the rhino went from thousands historically to ten individuals hanging on in Cameroon. By 2006, however, a survey found that none of the rhinos remained.
EDIT
http://news.mongabay.com/2010/0103-hance_extinct.html