The third season of Meerkat Manor premiaired in 2007. Season 3 has 13 episodes, each running for approximately 30 minutes. This season was the most famous of the series, as it featured the death of beloved meerkats such as Flower and Mozart, causing many fans to quit watching. Regardless of the drop in audience, the show remained Animal Planet's most-viewed program.
- On Dangerous Ground
- The Mission
- Sister Act / Something's Got to Give
- The Death of Romance
- The Tale of Len and Squiggy / The Tale of Ren and Stumpy
- The House of Zappa / Sibling Rivalry
- Heavy the Crown
- Journey's End
- A New Day
- Farewell My Lovely
- Three Degrees of Separation
- The Graduate
- A Family at War
Flower - The dominant female of the Whiskers, wears a radio collar.
Zaphod - The dominant male of the Whiskers.
Rocket Dog - Flower's daughter who struggles to lead the Whiskers.
Maybelline - A rebellious daughter who competes for the position of dominant female.
Mitch - A brave son of Flower and Zaphod who often rescues pups.
Daisy - One of Flower's daughters who falls pregnant to Houdini and his Zappa companions.
Sophie - Mozart's daughter who often babysits and teaches pups how to hunt.
Jogu - One of Tosca's sons who helps to babysit.
McMurphy - One of Tosca's sons.
Lyric - A subordinate female.
Bananas - A babysitter for Len and Squiggy (only mentioned in the UK version).
Clive - A pup from season one who is now an adult.
Liz - She always supports her dad, Zaphod.
Lizzie - The only female of her litter. She favors the babysitter, Sophie.
Busta - A son who loves play-fighting with his brother.
Suggs - A son of Flower and Zaphod
Len - A small male pup who falls victim to a bird of prey.
Squiggy - A small male pup born with a deformed leg.
Hannibal - The one-eyed, vicious dominant male of the Commandos.
Nikita - The pup-eating dominant female of the Commandos.
Wilson - A young, inexperienced roving male.
Mozart - Flower's resilient daughter who competes for the position of dominant female.
Kinkaju - Flower's daughter who competes for the position of dominant female.
Carlos - The dominant male of the Starsky who suffers from a wound.
Shady - A younger member of the group.
Houdini - The "Don Juan" of the desert, later becomes the dominant male of the Zappa.
Lola - The dominant female of the Zappa who was later overthrown.
Punk - The sister of Lola, she assumes the position of dominant female.
Frank - A large male and dominant male, until he's overthrown by Houdini.
Melanie - An evicted female who mates with Jogu.
Axel - A pup who is abandoned, but later adopted into the Whiskers.