Since 2009, every at the end of year, I always posted top 10 best selling manga in Japan, and this is the time for 2016 to get the rank.
As usual, Eiichiro Oda's manga One Piece get the top position with 12,314,326 copies which the sales duration is from November 23, 2015 to November 20, 2016. Second position reach by Assassination Classroom with 6,887,192 sales. This year, One Piece sales is really far from the second position.
The top 10 list you can see below.
|No||Manga Title||Author||Publisher||Total Sales|
|1||One Piece||Eiichiro Oda||Shueisha||12,314,326|
|2||Assassination Classroom||Yusei Matsui||Shueisha||6,887,192|
|4||Attack on Titan||Hajime Isayama||Kodansha||6,544,081|
|6||The Seven Deadly Sins||Nakaba Suzuki||Kodansha||5,115,573|
|7||My Hero Academia||Kōhei Horikoshi||Shueisha||5,114,916|
|8||Tokyo Ghoul:re||Sui Ishida||Shueisha||4,278,599|
|9||One-Punch Man||One / Yuusuke Murata||Shueisha||3,979,760|
|10||Food Wars: Shokugeki no Sōma||Yūto Tsukuda / Shun Saeki|
/ Yuki Morisaki
Different from the previous years, since 2009, One Piece always compete with Naruto, but this year the Masashi Kishimoto manga not listed because the manga series has completed.
Source: Oricon via ANN