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The Lost World: Jurassic Park and Jurassic Park III both take place on Isla Sorna. However, the two films feature almost entirely different dinosaur species. Where did all the new dinosaurs in Jurassic Park III come from and what happened to all the dinosaurs from The Lost World?

All these dinos appear in TLW:JP but not JPIII:

• Gallimimus


• Mamenchisaurus


• Pachycephalosaurus


• Edmontosaurus

All these dinos appear in JPIII but not TLW:JP:

• Ankylosaurus


• Brachiosaurus


• Ceratosaurus


• Corythosaurus


• Spinosaurus

Additionally, the group of raptors appear to be different in each film.

In Universe

Because the 3rd movie is on a different part of the island from the second.

From the script of The Lost world: (showing that some of the dinosaurs gathered in different parts of the island)

LUDLOW (cont'd) Our infrareds show their nesting sites are concentrated in the island interior. That's why we planned on
keeping to the outer rim.

Offering weak support for this as well is this excerpt from JP3 wiki:

The landscape of Isla Sorna is very drastically different from that in
The Lost World. [snip]..., although this could be because the parts of the
island seen here are in the lowlands of the island which is tropical,
while the sections scene in TLW is only from the highlands of the
island.

The other part is also explained in the script for JP3. There were things that InGen was doing that were not disclosed to the public.

GRANT Not with that sail. (Billy gives up) Spinosaurus
Aegypticus.

BILLY I don't remember that on InGen's list.

GRANT That's because it wasn't on their list. Who knows what else they were up to?

Out of Universe is the real answer

JP3 was not based on a book by Michael Crichton, unlike the first 2, and while it had some material from his novels it obviously was going to be different coming from script writers and not a novelist.

As for the appearance of dinosaurs changing, this is actually due to scientific finds during the period between films. Our view of Deinonychus* changed out of universe and they decided to be more scientifically accurate instead of keeping the look for continuity.

*The basis for JP raptors.

According to the Dinosaur Protection Group website created as part of the Jurassic World: Fallen Kingdom promotional campaign, Masrani Global Corporation secretly developed new dinosaurs on Isla Sorna between TLW:JP and JP3. The site explicitly lists every new dinosaur from the question except for the Brachiosaurus, which might simply have been elsewhere on the island in TLW:JP. The new velociraptors are however still unexplained.

Information surrounding the illegally bred species surfaced online during the 2015 inquiry via an anonymous hacker known as: JUR@55!_H@K3R, who published sensitive InGen documents. Key revelations included:

■ The new species were grown in secret on Isla Sorna (Site B) and experimented on over a period of nine months, starting just 100 days after the company was bought by Masrani Global.

■ Incubation was achieved covertly and quickly to evade attention; only a select few InGen members were involved, and their names have been removed from records. It is unclear whether Masrani Global’s CEO, the late Simon Masrani, was aware of the violation of law.

■ The research and growth of these animals were filed under “Early R&D for Jurassic Park’s second incarnation” and simultaneously “Amalgam Testing.”

■ The new species included: Ankylosaurus, Ceratosaurus, Corythosaurus, and Spinosaurus. All were abandoned on Site B, until the surviving animals were reportedly moved to Nublar to be housed as future attractions at Jurassic World.

■ A number of these new animals had originally been reported by the survivors of the plane crash on Isla Sorna during the summer of 2001, but the information was quickly buried by “bribed officials.”

Another page on the site explains that the island's original dinosaur population dropped quickly after Masrani's introduction of new dinosaurs, explaining why certain dinosaur species from TLW:JP didn't reappear in the sequel.

The operation to move the surviving animals from Isla Sorna to the park site on Isla Nublar was critical to their well-being. A considerable and mystifying drop in population on Isla Sorna had recently been discovered; some paleontologists claimed it was the result of territorial disputes, others argued disease was the catalyst, while some scientists even placed the blame on the animals’ behavior. Recent revelations linked to the corruption of the Gene Guard Act by members of Masrani Global confirm the true cause – the introduction of illegally cloned animals on the island in 1999 caused a profound impact on the ecosystem