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I just started watching The Flowers of Evil, and I just noticed that the anime was produced before the end of the manga. If that's the case, it seems reasonable to conclude that some manga plot points might have been omitted from the anime.

Given this, how much of the manga plot is covered in the anime? (Approximately which portions of the manga have been covered there, and does the plot diverge anywhere?)

Toshinou Kyouko
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Maroon
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The anime being only 13 episodes long covers up to chapter 20 (page 101 in volume 4, with chapter 20 being the second chapter in this volume). In the second part of the 13th episode we see a preview of the next season and the moments shown are mainly from the 5th and 6th volume. {Source: I own all of the translated volumes and have watched the anime} Aku no Hana (The Flowers of Evil) original manga by Shuzo Oshimi was recently concluded at 11 volumes.

As for the second part of your question, the anime staff have taken quite a few liberties in the direction of the anime. Major plot points are of course included in the anime adaptation. The main plot is the same, but as with many anime adaptations some scenes were cut off, others were a little changed. What is more, some reactions from the characters are different in some scenes, which gives the viewer a slightly different image of the character. I can't give you specific differences though (which as I said don't alter the plot, so no worries there), without possibly spoiling the story for you, as you didn't mention how many episodes of the anime you have watched.

Also, a special episode at the end of volume three isn't included in the anime adaptation and I doubt it will be, except perhaps as an OVA, as it is a small story about Nakamura and another guy back in middle school.

One major difference, irrelevant to the plot, is the artwork, which is absolutely different, and as a result the "feel" of the characters and the atmosphere that both versions give to the audience/reader are different.

Knowing that this shouldn't be part of my answer, I would however strongly recommend reading the great manga that Aku no Hana is.

Sahaquiel X
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    Feel free to give some examples of specific differences (since that might be useful in the future or for other people) - just use the [spoiler markdown](http://meta.stackexchange.com/a/72878/261498). – Maroon Jun 22 '14 at 12:04
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    Just wanted to emphasize the last two paragraphs of the answer: The anime and manga both have a different feel to them. I would suggest enjoying both of them. The manga just finished, and is considerably longer than the anime, so you might want to watch the anime first, or read the manga alongside the anime (which is what I did). The anime really captures the atmosphere that the manga builds. I hope they eventually animate the rest of the story. – Az- Jun 22 '14 at 15:32