- The name of Tom Felton's character Dodge Landon is a reference to the characters Dodge (Jeff Burton) and Landon (Robert Gunner), Colonel Taylor's (Charlton Heston) fellow astronauts in the original.
- The orangutan character befriended by Caesar in prison is named Maurice after actor Maurice Evans, who played the orangutan Doctor Zaius in Planet of the Apes (1968) and Beneath the Planet of the Apes (1970).
- The name given to Caesar's mother is "Bright Eyes" due to the coloration in her eyes caused by the ALZ-112 virus. "Bright Eyes" is the name given to Taylor (Charlton Heston) by Dr. Zira (Kim Hunter).
- A news headline reports that the "Icarus" is the first craft headed to Mars. This is the most popular fan-proposed name of Taylor's craft, and refers to the Greek myth which cautions against overreaching ambition.
- Dodge Landon speaks two of Charlton Heston's most famous PotA lines: "It's a madhouse! A madhouse!" and "Take your stinking paws off me you damn dirty ape!"
- Clips from Charlton Heston in The Agony and the Ecstasy (1965) and The Ten Commandments (1956) are shown.
- In one scene, Caesar is shown handling a 3D puzzle of the Statue of Liberty, in reference to the the original ending.
- The gorilla Buck is named after Buck Kartalian who played Julius the gorilla and another gorilla, Frank, from Conquest of the Planet of the Apes (1972).
- One of the female chimps is "Cornelia", named for Dr. Cornelius of the original.
- The gray, hairless chimpanzee Rocket, who is Caesar's right-hand man, is named after Norman Rockett, the set decorator of the original.
- The lab worker who cares for the chimps is named Franklin, a nod to director Franklin J. Schaffner.
- Jamie Harris plays Rodney, the sympathetic keeper in the ape sanctuary, named for original ape actor Roddy McDowall.
- Late in the film we are told that the spacecraft and astronauts have disappeared. We can assume that they gone into a time warp and will end up on the future "Planet of the Apes".
- The police riding their horses between the cars while striking apes mirrors a scene near the beginning of the original where apes on horses corral humans.
- The San Bruno Primate Sactuary is nod to the human zoo from the original film.
- The fight between Rocket (Terry Notary) and Caesar (Andy Serkis) was a nod to the fight between Taylor (Charlton Heston) and another captive human from the original.
- Koba the bonobo is based on Aldo the gorilla, main villain of Battle for the Planet of the Apes (1973) with his hatred of humans.
- Dodge hoses Caesar just as Julius hosed Taylor.
- When Caesar releases the apes from their cages at the sanctuary, Rocket (Terry Notary) is in the same position and expression Leo Davidson had from Tim Burton's version of Planet of the Apes (2001).
- The first word spoken by an ape is "no". This was a pivotal line in Escape from the Planet of the Apes (1971), Conquest of the Planet of the Apes (1972) and Battle for the Planet of the Apes (1973).
- When Caesar is on horseback and the SWAT officer is amazed, this is a nod to the hunt scene from the original where Taylor was stunned seeing a gorilla on horseback.
- Dodge Landon's (Tom Felton) personality is based on Julius from the original, for being jailer of the animals, torturing them, and having a certain dislike to the main protagonist.
- A woman on Will's team is named Linda, this a nod to Linda Harrison who played the mute Nova in the first two films and Zira from the makeup test.
- Caroline says ''I love chimpanzees.'', which was a line Armando said in Escape from the Planet of the Apes (1971).
- Dr. Steven Jacobs is an allusion to Arthur P. Jacobs, producer of the original films.