The characters of the Japanese visual novel "Popotan" were designed by Akio Watanabe under the alias Poyoyon♡Rock, and the characters in the anime adaptation were designed by Rondo Mizukami and based on Akio Watanabe's original concepts for the visual novel. The series takes place on a fictional Earth in which exist supernatural beings with powers and follows three such supernatural sisters as they travel through time in a mansion, searching for the reason for their journey. Though many of the characters in the visual novel share personality traits and character relations with their anime counterparts, there are numerous differences between the two media. Both the visual novel and anime have mutually exclusive characters in addition to the changes in character roles.
In the visual novel, the player controls Chris, a slacker who roams from town to town until he comes across the unnamed town that is the setting of "Popotan". The story centers on him as he moves in with three sisters and their maid (all of whom become the protagonists for the anime) and his transformation in his lifestyle. In the anime, the primary protagonists of the series are the three sisters, Ai, Mai and Mii. Ai is a compassionate, motherly figure whose overly compassionate nature often causes problems. Mai is a tomboy who wishes for the quest to end and to live a normal life. Mii is an energetic child who likes to cosplay and help people in trouble. Early on, the series explored the characters' personalities by focusing on a single character per episode. The sisters' maid, Mea, is portrayed as a secondary protagonist in the anime, but is portrayed as a primary protagonist in the radio drama that is a continuation of the anime.
Main characters.
Chris.
 is the protagonist of the story whom the player controls. He is a high-school dropout and slacker who gave up on the world. He wanders from city to city playing his guitar to make just enough money to cover his living expenses. He moves in with the three sisters because they charge cheap rent and he likes staying in a house full of girls; however, he quickly learns he must change his slacker ways. As the game progresses, Chris has the possibility of developing a romantic relationship with one of the girls; at first this is limited to the three sisters: Ai, Mai and Mii, but after completing at least one of their routes, five other girls will be accessible. Since the visual novel revolves around him, the only time his character is seen is during event sequences; however, in the fan disc, his image is visually represented along with the other characters.
Sisters.
In the visual novel their roles are as principal romancable characters for the protagonist while in the anime they, along with their maid, Mea, take on the roles of the protagonist. The three sisters, Ai, Mai and Mii, all have supernatural powers that differ based loosely on their personality type. All three live together under the same roof of a Western-style mansion with a maid helping take care of their needs.
Ai.
, the oldest sister and acting landlord of the mansion. Aged 18, she is the only major character with large breasts and often wears a Santa Claus-style hat over her green hair. She is near-sighted and needs glasses to see clearly; additionally, she has a no sense of direction. Ai is a motherly figure and constantly tries to help people. She does most of the chores their maid does not, and, loves to cook despite being an incompetent. Her easygoing caring nature often leads her to fail things because she cannot muster the resolve to criticize others. Believing she is ugly and fat, Ai wears clothing and glasses to hide behind. This is why she allows Chris to stay with them when she finds out he has nowhere else to go. Ai also loves to take baths, more than once a day if possible. She also seems to be the de facto caretaker of the sisters' pet ferret, Unagi, which hides under her hat. Ai has the ability to speak to plants, specifically dandelions, which she and her sisters refer to as "popotan".
In the anime, Ai becomes accustomed to the time traveling and non-aging and is mostly unaffected by it until she meets Daichi as an adult. She uses her ability help them find Shizuku, whom the sisters are searching for. Ai is voiced by Mayu Fujisaki in the visual novel; in the anime she is voiced in Japanese by Sayaka Ohara and in English by Nicole Oliver.
Mai.
, the middle sister at 14, has pink hair and usually wears sporty clothes. Mai is constantly reminded of her small breast size by her younger sister Mii, which causes her to lose her temper. Mai goes to school with Mii and has a friend there, Konami, who knows Chris from the past. Although she is the middle sister, Mai governs household affairs such as the budget. She longs to leave the mansion but does not want to burden Ai whom she knows does not have the willpower to deal with such responsibilities. Mai has a tomboyish personality and is very short-tempered, especially when it comes to Chris, the more so when she thinks she'll lose face. She is the only character who vehemently opposes Chris's staying at the mansion, despite the fact that he pays rent.
Mai's role is more prominent in the anime. Early in the season she had problems with constantly moving; because she thought everyone hated her after making friends and then abandoning them, she became so depressed that she refused to go to school. She understood the impact of their journeys on others, but unlike Ai, did not have the maturity to cope with it. Early on in the series she makes friends with a classmate of hers, Konami. When it was time for Mai to leave, Konami helped convince Mai that she was wrong and in consolation Konami left a sketch portrait of Mai she made for a class assignment as a departing gift stating that they will remain friends forever, even if they never see each other again. While waiting for Mai's return, Konami dies two years before the mansion is in a location where the two could meet again. Later in the series, Mai meets Konami's daughter; she initially mistakes her for Konami but quickly learns her name is Mai and that she was named by Konami in memory of her friend. Mai discovers that Konami's daughter has more in common with her than a name: she, like her namesake, feels that everyone hates her. As a result, Mai feels it her duty to both Konami and her daughter to show her that way of thinking was wrong, just as Konami did for her. Mai ultimately gave up and failed at the time when she Konami had still been waiting for her even as she lay dying. This, compounded with Keith's words about the pain the girls bring to others, reawakening her depression in a much deeper manner. When she returns to visit Konami later and leaves, as a departing request, asks Konami to explain to her daughter what she felt so that she would not follow the same path as the younger sister Mai. Along with Mea, the maid, Mai is left at one point when the mansion disappears into the future without them. It is during this time that Mai realizes that she cannot age and Ai explains the connection to the mansion and aging process. Mai is voiced by Mio Oukawa in the visual novel; in the anime she is voiced in Japanese by Masumi Asano and in English by Nicole Bouma.
Mii.
, the youngest sister at 11, has light purple hair that is often tied in a double-bun on her head, except when she cosplays as "Magical Girl Mii"; she then wears it in twin pony-tails. Mii goes to the same school as Mai. She goes around asking Chris to play with her almost anytime she sees him and loves to cosplay as a magical girl, "Magical Girl Mii", trying to help others out around town, though the results often vary. The game has more sexual scenes involving her than any other character. She tries to have sex with Chris early on and has sex with Mea, the maid, a few times.
Mii is not as lascivious in the anime, though she has an obsession with defining plushy things, especially Ai's breasts. She also loves to compare breast sizes of various females. Also, though she passes through time like the rest of the girls, her very naivete and energy allow her to overcome most of the jumps with ease.
"Magical Girl Mii" was used in the anime, though its origins were changed. In the anime it was a specialized cosplay costume she had created to mimic a magical girl television show which cost a lot of money, but Ai seemed easily able to pay for it. That episode she met a chronically ill girl named Miyuki and attempted to cheer up. After this, she wears it around and pretends to help stop evil and believes she has superpowers. Later during the episode, Miyuki collapsed from overexertion playing with Mii. Mii tried to use powers she thought she had to heal her. The attempt was successful, and Ai revealed to the viewers that Mii's special power was healing. However, Mii remains unaware of this for a good portion of the season, and continues to believe that she has other powers as well. After the episode, Mii continues to cosplay in the outfit with the same type of antics. Mii is voiced by Toromi in the visual novel; in the anime she is voiced in Japanese by Momoi Haruko and in English by Jocelyne Loewen.
Mea.
, the sisters' maid, who is sometimes referred to as Mare in the visual novel and Mear in the fan book, is actually a lifelike android that has existed for a long time. Her scarlet hair is tied down into two long pigtails that reach her elbows. She appears completely unemotional, especially at the beginning of the game, but she has her own desires and becomes friendlier with Chris as the story progresses to varying degrees depending upon whether it's her balls or not.
In the anime, Mii constantly points out Mea's small breast size, though she does not lose her temper like Mai. She also has a voracious appetite despite her diminutive figure. She starts out more robotic-like, but becomes less so as the story progresses, such as in Episode 4 when she becomes concerned and fixes the doll of a malevolent-but-lonely child's spirit and seems to make some emotional connection to it. These scenes though are largely seen only by the audience and not by any of the major characters. Mea is left behind with Mai when the house vanishes after visiting the hot springs. She and Mai later rejoin the group, when the mansion returns five years later to the same spot. While waiting for the mansion to return, she works as a rental maid in the area to keep things up with Mai. It is later revealed that Mea is a "guard" sent to help the girls along their journey and that Mea is working with Shizuku under Keith.
While Mea is listed officially as an android for the anime, it is unclear while watching "Popotan" that this is the case as there is no given reference, beyond her personality, to that effect. In episode four it is revealed she is not human, but the episode does not state what she is. Mea is voiced by Asumi Noda in the visual novel; in the anime she is voiced in Japanese by Mai Kadowaki and in English by Anna Cummer.
Shizuku.
 can be recognized by light-green hair and a similarly colored poncho. Her calm, mature demeanor contrasts with her youthful appearance, and her age is never mentioned. Chris meets her on a stroll at night and brings her back to the mansion. She lacks linguistic skills, and at first not much about her is learned. Because Shizuku is unable to take care of herself, Chris offers to pay her rent as well.
In the anime, Shizuku is the reason for the girls' travels. She is portrayed as a goddess of the dandelions;