While in the US government bunker, the apes come upon a doll that goes "Mama" in the same voice the doll that Taylor found in the 1968 film which increases the realization that humans once were the dominant species of Earth.
Kingdom of the Planet of the Apes is set 300 years after War for the Planet of the Apes in the Southern California area. Raka's residence is set underneath the ruins of LAX. The clan of Noa reside somewhere within the Los Angeles basin. Proxima Caesar's clan reside near the remains of the Coronado Bay Bridge near San Diego, CA. The observatory is heavily implied to be the Griffith Observatory, based in the Hollywood Hills. This is a nod to the original film saga as the Los Angeles basin is the setting for Escape from the Planet of the Apes, Conquest of the Planet of the Apes, and Battle for the Planet of the Apes. The first films in the "Caesar trilogy" were also set in and around San Francisco and the nearby Muir Woods National Park.
Raka calls Mae Nova, stating that apes name all humans Nova. Nova was the name of the mute human adopted by Maurice in War for the Planet of the Apes. Nova is also the name of Taylor's human mate in the original 1968 Planet of the Apes.