Main article: Kowalski & Skipper
Kowalski is Skipper's second in command, friend and brother figure. Skipper always looks to Kowalski for options and usually follows it. However, there are times when Skipper gets irritated with Kowalski's ideas, finding them sometimes ridiculous. The few times he doesn't ask for Kowalski's ideas was when he refused to hear options from Kowalski because he got them in the situation in the first place.
Kowalski is usually a replacement as leader for Skipper whenever their leader is unavailable. An example is in "I Was A Penguin Zombie" where everyone believed Skipper was dead and Kowalski took over temporarily until he was revealed alive in the end of the episode).
Main article: Skipper & Rico
As children, Rico helps Skipper come up with their signature flipper slapping called the "high one." Because of his useful storage, Skipper comments that Rico is a "valued member of [their] team. They both have a love of destruction in the series, while it lacks in the films. However, in "Kaboom and Kabust" Skipper's love for destruction is not as strong as Rico's. He also fears that if Rico goes through stunts too much, then he'll overreact with it and do harm not only to others, but also to himself.
Main article: Private & Skipper
Private is the youngest of Skipper's brothers.
Ever since Private was a child, Skipper has loved him and called him adorable (which got annoying to Private after ten years of hearing it come from Skipper's mouth. Even though Skipper is hard at times, he has a soft spot for Private. In "When the Chips Are Down", Skipper thought they truly lost Private and began grieving for him, but immediately cried and later hugged Private, telling him to never scare Skipper like that ever again. During the film, Skipper continues treating him like a tagalong. He then endangers Private when he has him as the distraction to stop Dave and ends up getting Private kidnapped by the mad scientist. Skipper later becomes determined to save him from Dave, and becomes very distraught when the medusa serum seemingly kills Private. Skipper believes that Private is dead after he fails to call them through the upper level.
Main article: Skipper & Julien
Hans is the reason why Skipper isn't allowed in Denmark. He once attempted to replace Kowalski, Rico and Private, but Skipper caught on and rejected him. He has revenge on Skipper again when partnering with Dr. Blowhole. which led to Skipper's almost downfall. Later, the puffin and him are considered "frenemies".
There are hints that Hans is homosexual and has a crush on Skipper.
Out of all the penguins, he has the greatest animosity against Skipper. Blowhole calls him his "number one enemy". Skpper dislikes Blowhole very much and defeated him numerous times.
Skipper did not know Dave after their first encounter when he, Kowalski, Rico and Private were children. They stayed there long enough for Dave to know their names. However, Skipper hardly remembers his name unless someone corrects Skipper the guy's real name. However, Skipper grows worried when Dave kidnapped Private and the ohter Shanghai penguins and wishes to bring him down. Especially after believing Private to be killed, Skipper hates him. Then, seeing Dave in the globe and gives him away to a little girl. Also thinking he was married
Kitka is one of the few female characters whom Skipper had been attracted to. They briefly dated and holds that she isn't responsible for snatching King Julien. He breaks up with her after Kitka eats Fred the Squirrel.