The story starts in a small town in Gunma Prefecture[4] and follows Takao Kasuga, a middle school bookworm whose favorite book is Charles Baudelaire's Les Fleurs du mal.

When his mother finds out he was responsible for the vandalism, he runs from home and attempts to bike with Nakamura past the mountain adjacent to the town.

At the start of summer vacation, they create a plan to nail the panties to a piece of plywood to display at the upcoming festival.

Saeki later turns herself in to the police for setting the fire, prompting her best friend Ai Kinoshita to tell their school about Kasuga's crimes.

Kasuga finds his classmate Aya Tokiwa looking at Les Fleurs du mal in a used bookstore and she starts lending him novels, rekindling his love of literature.

They take the train to Tokawa Station in Chōshi, Chiba and find her eatery, where her mother warns them that Nakamura is "peaceful now", but Tokiwa insists on speaking to her.

After falling asleep with Tokiwa, Kasuga dreams of the wilting flower of evil, its scar no longer present on his hand.

In his dream he envisions the futures of the series' characters; he marries and has a child with Tokiwa, Saeki starts her own family and reunites with Kinoshita, and Nakamura finds contentment, eventually moving away to the city.

Oshimi first read Charles Baudelaire's Les Fleurs du mal in middle school and found the book to feel "suspicious, indecent, yet nastily noble".

[5] Oshimi also makes references to other artists such as with the cover of the tenth chapter parodying Francisco Goya's The Clothed Maja.

[7] After the publication of the second volume of the manga, Oshimi learned of the French film Don't Deliver Us from Evil and in retrospect he felt he could relate to the themes of the film where "the girls worship Baudelaire and Lautrémont, create a kingdom of evil all for themselves, and fall into ruin..."[8] Oshimi drew on many aspects of his life for the manga such as the settings and characters.

The settings are based on real locations from Oshimi's hometown including: the school library,[9] the riverbank,[10] and the park where Kasuga is splashed with water.

[12] Initially, the director Hiroshi Nagahama declined the offer to direct the anime because he felt it would be best presented as live-action, but reconsidered when he figured out how to adapt it and pitched the idea of using rotoscoping.

[16][17] Nagahama knew that the rotoscoping would be controversial, but he felt it was worth it because it would make the anime leave an impact, even if it was viewed as "creepy".

[35] The opening theme is "Aku no Hana" (惡の華) by Uchūjin with guest vocalists Noko, Mariko Gotō and Shiho Nanba [ja].

[39] The film is directed by Noboru Iguchi, with a screenplay by Mari Okada and music by Yasuhiko Fukuda starring Kentaro Ito.

[57] Anime News Network (ANN) editor Carl Kimlinger gave the series high praise when it was streaming, giving credit to both director Hiroshi Nagahama and composer Hideyuki Fukasawa for doing Oshimi's work justice with direction that is part psychological thriller and darkly romantic with the inclusion of rotoscoping and a score that is atonally sinister, saying that, "[I]t is a series that can be attacked from any direction and not crack.

"[58] Fellow ANN editor Nick Creamer also liked the series, praising the story for conveying themes of human identity and codependence with amoral people and the direction for its slow and methodical pace, concluding that "The Flowers of Evil is one of the best shows of recent years, an absurdly confident mood piece with a uniquely effective aesthetic and a true understanding of and sympathy for the emotional trials of youth.

"[60] Tim Jones, writing for THEM Anime Reviews, was also put off by the rotoscoping style, saying that from a distance it looks "comical and oft-putting (sic)."

But Jones gave praise to the cinematography, the main trio's development and Nagahama's direction on a typical high school setting.

[61] Chris Beveridge of The Fandom Post wrote: "This has more life to it, more meaning to it, than pretty much the majority of shows out there because of the acting, the story and the presentation.

"[62] Ink of Otaku USA chose the series as his pick for the Top Anime of 2013, praising the performances, sound design, pacing and rotoscoping technique for delivering "an oppressive atmosphere of anxiety" in a high school setting, concluding that, "If you like slow, moody pieces, Flowers of Evil is a must!