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LilieThe main protagonist of Atelier Lilie. Lilie is a young and aspiring alchemist from the city of Kentonnis on the Isle of El Bador. She possesses no last name, for she is an orphan; much like Ingrid and Hermina, she was raised as a foundling by the Kentinnis Academy of Alchemy. She is one of Dornier's finest students as Atelier Lilie opens. In the opening of the game, Dornier is charged with opening an academy of alchemy in the city of Salburg, and he asks Lilie to come along to assist in this endeavor.
Elsa HessenA young girl who calls herself a baker, though the bakers of Artisan Street haven't seen any person like her. She and Lilie quickly make friends with each other after they meet. She likes rum raisin. She recently came to Salburg from a neighbouring farming village and can often be seen curiously looking around the city. Elsa does not talk about her origins, and is actually from the aristocratic family of Maxheim and is the younger sister of Hedwig.
GerhardAn adventurer who likes to tweak equipment, and also enjoys apple pies and singing.
- Promoted to Playable: He's the young version of "Bukiya no Oyaji" from Marie and Elie.
Irma WalderA fortune teller that's part of a travelling caravan. She has traveled all over the country, but has few friends, and becomes fast friends with Lilie when the two meet. Irma is a friendly person with a bright and positive attitude. Her favorite thing is her set of tarot cards, which she has been using ever since she started telling fortunes. Her dream is to achieve perfect readings through her cards. She will go silent if her cards change during a reading.
Theo MohnmeierA young man who comes from a family of farmers who specialize in poppies. He spent most of his childhood working out in the fields, and has grown physically strong because of it. His family has never been wealthy, but he believes in working hard, even if it won't make you instantly rich. Now that Theo is older, he does less work at his family's fields and spends more time in Salburg. He enjoys spending time at the bar and being outside of his home. He has also now become an adventurer, although he has no prior battle experience. He is relatively new to the world of adventuring, but wishes to become stronger and more well known. His ultimate dream is to live within the city of Salburg and to have a lot of money. Like Lilie, he also loves beef jerky.
Ziska VillaA female warrior who has always dreamed of knighthood. Since childhood, Ziska has been fascinated with the Holy Knights. She wishes to become the first female Holy Knight, and will stop at nothing to reach her goal.
ChourouThe leader of the faeries.
DornierLilie's direct mentor figure, who is trying to establish the academy seen in "later" titles. As such, he can be constantly found in the atelier. If the player chooses to mentor Ingrid, he will mentor Hermina, and vice versa. He remains unplayable, however. Lilie can obtain recipe books from him for her alchemy.
EiorossA starving artist who came out of seemingly nowhere, Eiroross has a passion for painting. He specializes in landscape painting, and is very modest about his talents. He would truthfully like to start painting portraits, but has a difficult time finding people who would volunteer to be painted. He is always outdoors looking for inspiration to paint.
- Starving Artist: Eioross always seems to be down on his luck, and can barely afford to eat.
GemeinerA shady character who has lived alone in a desolate corner of Salburg for most of his life. He has very few possessions and is very poor. Because of this poor circumstances in life, Gemeiner has turned to swindling the people of Salburg for money. Upon hearing about Lilie's efforts to create the academy, Gemeiner takes it as the perfect opportunity to make some cash.
Hedwig MaxheimAn aristocrat living in Salburg, and Elsa Hessen's older sister. Her family has never been short of money, and so Hedwig has never had to work in her life. She hasn't yet learned the value of doing things for herself, and so she has grown up to be a very spoiled and uptight individual. She has grown bored of her current life and is always waiting for something interesting to happen.
Heinz MaddokThe owner of the adventurer's bar "The Golden Wheat".
HerminaA child prodigy, and literal genius. At the age of ten she shows remarkable skills in alchemy and has already been enrolled in the academy of El Bador; her talent was discovered because she is an orphan who was raised as a foundling by the El Badoran academy. She was raised alongside Ingrid, another highly talented orphan student, and even at this time the two share a love-hate relationship
- Recurring Character: She appears in Elie, Lilie, Judie, Marie & Elie, Marie Elie & Anis and her own title Hermina and Culus: Atelier Lilie Another Story, giving her an impressive record of six nearly-consecutive appearances between 1998 and 2003.
IngridA child prodigy. She has been studying alchemy since the age of eight, and shows remarkable progress for a girl that is only ten years old. She was born and raised in El Bador, and was taught at the renowned Kent Academy alongside Hermina, another child prodigy who is the same age. Although the two were practically raised together, they see each other as rivals and do not get along. The two can rarely agree on anything and argue often. The rivalry is life long, and the two are still bitter towards one another in Atelier Elie after they've both aged nearly 30 years.
- Cutting Off the Branches: Ingrid is a major supporting character throughout the game, and can be chosen as Lilie's "primary" assistant (the other option being Hermina); other games and side materials make it clear that Ingrid was canonically chosen for this role.