A team of researchers funded by a New York pharmaceutical firm Wexel Hall, including Dr. Jack Byron, Gordon Mitchell, Sam Rogers, Gail Stern, Cole Burris, and Dr. Ben Douglas leave for a jungle in Borneo to search for a "blood orchid", a flower they believe can be used as a type of fountain of youth. Though their guide Captain Bill Johnson and his partner Tran has misgivings about which path to take, Jack convinces him to take an unsafe path. The team goes over a waterfall and has to wade through the river. A giant anaconda emerges from the water and swallows Ben whole, but the rest of the team escape from the river. Bill assures them that it was the largest snake he has ever seen and that it should take weeks for it to grow hungry again. However, most of the team demand that the expedition be called off. They travel to Bill's friend, John Livingston, who lives on the river, to see if Johnson can borrow his boat but they find Livingston dead and his boat crashed.
They find themselves in a small native village consisting of thatched huts and a disemboweled anaconda with a pair of human legs hanging out of the snake's abdomen. The team realizes that the snakes are unusually large in size because their lives have been extended through the orchids, which are a part of the local food chain. Jack says that since they must be close to the orchids, they should press on. However, the others contend that there is no evidence that the orchids will have the same effect on humans. Wanting to leave, they start building an escape raft.
Gordon discovers Livington's radio and gun and realizes they could have called for help long ago. Jack is unable to convince him to allow the expedition to continue, so he paralyzes him using a poisonous spider. As Jack joins the others at the raft, Sam discovers Gordon and the spider bite. An anaconda drops down from the rafters and swallows Gordon alive soon after she leaves the building. The others arrive just as it finishes, so Bill sets the building on fire in hopes of killing the anaconda but notices that it already made its escape. Jack uses the commotion to steal the raft.
With no more material to make another raft, they hack through the jungle to beat Jack to the orchids and retrieve their raft. On the way they fall into a cave trying to escape from an anaconda. Cole gets lost and panics after finding a skeleton. He runs into Bill's partner, Tran, and as they return to the others, Tran gets pulled under and Cole tries to find him but all he sees is Tran's lost flashlight floating. Tran is eaten by an anaconda under water. Bill tries to find Cole and Tran but also notices Tran's lost flashlight floating but with his blood surrounding it. The terrified Cole escapes from the caves behind the group, seconds ahead of the snake, which follows him through the hole and gets stuck. Sam uses a machete to behead it, but another snake captures Cole. The team follows and find him being constricted but still alive. Bill throws his knife and impales the snake through the head, killing it and freeing Cole.
The group finds the raft just as Jack finds the blood orchids, hanging precariously above a pit in which a ball of male anacondas are mating with the queen. Jack shoots Bill in the arm and forces the party to accompany him to the orchids. He has Sam cross the pit via a thin log to fill a backpack with orchids. As she returns, the log cracks. Jack orders her to throw him the backpack, but Sam threatens to drop the flowers into the pit unless he drops the gun. The log breaks, and she falls, landing halfway down the pit. As the others help her climb out, Jack attempts to retrieve the backpack. The spider he used to paralyze Gordon escapes from its jar and bites him. Jack falls into the pit and is devoured as Sam and the others escape.
The female anaconda notices them, but Gail tricks it into biting their fuel container. Bill tries to shoot the snake, but the gun is empty. Cole shoots it with a flare, causing a chain reaction that kills the snakes and destroys the blood orchids. Bill, Sam, Cole, and Gail make it back to the raft and leave.Johnny Messner as Bill Johnson
KaDee Strickland as Sam Rogers
Matthew Marsden as Dr. Jack Byron
Eugene Byrd as Cole Burris
Salli Richardson-Whitfield as Gail Stern
Morris Chestnut as Gordon Mitchell
Karl Yune as Tran Wu
Nicholas Gonzalez as Dr. Ben Douglas
Andy Anderson as John Livingston
The review aggregate site Rotten Tomatoes reported that the film received 26% positive reviews based on 117 reviews. Metacritic reported the film had an average score of 40 out of 100 based on 28 reviews. Roger Ebert awarded the film two out of four stars, a rating less than that he gave the original film. Ebert, however, praised the acting of Matthew Marsden as being "suitably treacherous".
Anacondas: The Hunt for the Blood Orchid was nominated for a Razzie Award for Worst Remake or Sequel, but lost to Scooby-Doo 2: Monsters Unleashed.