Japanese Order of Battle at Midway
Ship "Classes" in parenthesis.

COMBINED FLEET
Adm. Isoroku Yamamoto, in Yamato
Chief of Staff, RADM Matome Ugaki

Main Body, Admiral Yamamoto
BatDiv 1, Admiral Yamamoto
BB Yamato (flagship, Yamato), Captain
BB Nagato (Nagato), Captain Hideo Yano
BB Mutsu (Nagato), Captain Teijiro Yamazumi
Carrier Group, Captain Kaoru Umetani
CVL Hosho (Hosho), Captain Umetani
Air Unit (8 bombers), Lieutenant Yoshiaki Irikiin
DD Yukaze (Minekaze), Lieutenant Commander Shizuka Kajimoto
Special Force, Captain Kaku Harada
Chiyoda (seaplane carrier, Chitose), Captain Harada
Nisshin (seaplane carrier, Nisshin), Captain Katsumi Komazawa
Screen (DesRon 3), RADM Shintaro Hashimoto
CL Sendai (flagship, Jintsu), Captain Nobue Morishita
DesDiv 11, Captain Kiichiro Shoji
DD Fubuki (Fubuki), Captain Shizuo Yamashita
DD Shirayuki (Fubuki), Captain Taro Sugahara
DD Hatsuyuki (Fubuki), Captain Lieutenant Commander Junnari Kamiura
DD Murakumo (Fubuki), Captain Commander Hideo Higashi
DesDiv 19, Captain Ranji Oe
DD Isonami (Fubuki), Commander Ryokichi Sugama
DD Uranami (Fubuki), Commander Tsutomu Hagio
DD Shikinami (Fubuki), Commander Akifumi Kawahashi
DD Ayanami (Fubuki), Commander Eiji Sakuma
1st Supply Unit, Captain Shigeyasu Nishioka
Naruto (Oiler), Captain Nishioka
Toei Maru (Oiler)

GUARD (Aleutians Screening) FORCE, VADM Shiro Takasu in Hyuga
Chief of Staff, Rear Admiral Kengo Kobayashi
BatDiv 2
BB Hyuga (flagship, Hyuga), Captain Chiaki Matsuda
BB Ise (Hyuga), Captain Isamu Takeda
BB Fuso (Fuso), Captain Mitsuo Kinoshita
BB Yamashiro (Fuso), Captain Gunji Kogure
Screen, RADM Fukuji Kishi
CruDiv 9, Rear Admiral Kishi
CL Kitakami ( flagship, Kuma), Captain Saiji Norimitsu
CL Oi (Kuma), Captain Shigeru Narita
DesDiv 20, Captain Yuji Yamada
DD Asagiri (Fubuki), Commander Nisaburo Maekawa
DD Yugiri (Fubuki), Captain Masayoshi Motokura
DD Shirakumo (Fubuki), Commander Toyoji Hitomi
DD Amagiri (Fubuki), Captain Buichi Ashida
DesDiv 24, Captain Yasuji Hirai
DD Umikaze (Shiratsuyu), Commander Nagahide Sugitani
DD Yamakaze (Shiratsuyu), Commander Shuichi Hamanaka
DD Kawakaze (Shiratsuyu), Commander Kazuo Wakabayashi
DD Suzukaze (Shiratsuyu), Commander Kazuo Shibayama
DesDiv 27, Captain Matake Yoshimura
DD Ariake (Hatsuharu), Commander Shoichi Yoshida
DD Yugure (Hatsuharu), Commander Kiyoshi Kamo
DD Shigure (Shiratsuyu), Commander Noboru Seo
DD Shiratsuyu (Shiratsuyu), Lieutenant Commander Kimmatsu Hashimoto
2nd Supply Unit, Captain Matsuo Eguchi
San Clemente Maru (oiler), Captain Eguchi
Toa Maru (oiler)

FIRST CARRIER STRIKING FORCE (1st Air Fleet), VADM Chuichi Nagumo
Carrier Group, VADM Nagumo
CarDiv 1
CV Akagi  (flagship, Akagi) 21 Zero fighters, 21 dive bombers, 21 torpedo bombers (Sunk)
CV Kaga (Kaga) 21 Zero fighters, 21 dive bombers, 30 torpedo bombers (Sunk)
CarDiv 2 -- RADM Tamon Yamaguchi
CV Hiryu (flagship, Hiryu) 21 Zero fighters, 21 dive bombers, 21 torpedo bombers (Sunk)
CV Soryu (Hiryu) 21 Zero fighters, 21 dive bombers, 21 torpedo bombers (Sunk)
Support Group -- RADM Hiroaki Abe CruDiv 8
CA Tone (flagship, Tone)
CA Chikuma (Tone)
2nd Section, BatDiv 3 --
BB Haruna (Kongo)
BB Kirishima (Kongo)
Screen (DesRon 10) -- RADM Susumu Kimura
CL Nagara (flagship, Nagara)
DesDiv 4 -- 4 DDs
DesDiv 10 -- 3 DDs
DesDiv 17 -- 4 DDs
Supply Group -- 5 oilers, 1 DD

MIDWAY INVASION FORCE, (2nd Fleet), VADM Nobutake Kondo
Invasion Force Main Body
CruDiv 4 (less 2nd section)
CA Atago (flagship, Takao),
CA Chokai (Takao)
CruDiv 5 (less 2nd section)
CA Myoko (Myoko)
CA Haguro (Myoko)
BatDiv 3 (less 2nd section) --
BB Kongo (Kongo)
BB Hiei (Kongo)
Screen (DesRon 4) -- RADM Shoji Nishimura
CL Yura (flagship, Nagara)
DesDiv 2 -- 4 DDs
DesDiv 9 -- 3 DDs
Carrier Group Zuiho (CVL) -- 12 Zero fighters, 12 torpedo bombers; 1 DD
Supply Group -- 4 oilers, 1 repair ship
Close Support Group -- VADM Takeo Kurita
CruDiv 7
CA Kumano (flagship, Mogami)
CA Suzuya (Mogami)
CA Mikuma (Mogami) (Sunk)
CA Mogami (Mogami)
DesDiv 8 -- 2 DDs 1 oiler
Transport Group -- RADM Raizo Tanaka
12 transports carrying troops
3 patrol boats carrying troops
1 oiler
Escort (DesRon 2) -- RADM Tanaka
CL Jintsu (flagship, Jintsu)
DesDiv 15 -- 2 DDs
DesDiv 16 -- 4 DDs
DesDiv 18 -- 4 DDs
Seaplane Tender Group -- RADM Riutaro Fujita
Seaplane Tender Div 11
Chitose (CVS) -- 16 fighter seaplanes, 4 scout planes
Kamikawa Maru (AV) -- 8 fighter seaplanes, 4 scout planes
1 DD;
1 patrol boat carrying troops
Minesweeper Group
4 minesweepers
3 submarine chasers
1 supply ship
2 cargo ships

NORTHERN (Aleutians) FORCE (5th Fleet) -- VADM Moshiro Hosogaya
Northern Force Main Body
CA Nachi (flagship, Myoko)
Screen --
2 DDs
Supply Group --
2 oilers, 3 cargo ships
Second Carrier Striking Force -- RADM Kakuji Kakuta
Carrier Group (CarDiv 4)
CVL Ryujo (flagship, Ryujo) -- 16 Zero fighters, 21 torpedo bombers
CV Junyo (Junyo) -- 24 Zero fighters, 21 torpedo bombers
Support Group (2nd section, CruDiv 4) --
CA Maya (Takao)
CA Takao (Takao)
Screen (DesDiv 7) --
3 DDs
1 oiler
Attu Invasion Force -- RADM Sentaro Omori
CL Abukuma (flagship, Nagara)
DesDiv 21 --
4 DDs
1 minelayer
1 transport carrying troops
Kiska Invasion Force -- Capt. Takeji Ono
CruDiv 21 --
CL Kiso ()
CL Tama ()
AMC Asaka Maru (auxiliary cruiser)
Screen (DesDiv 6) --
3 DDs
2 transports carrying troops
Minesweeper Div. 13 --
3 minesweepers
Submarine Detachment -- RADM Shigeaki Yamazaki
SubRon 1 -- I-9 (flagship)
SubDiv 2 -- 3 submarines
SubDiv 4 -- 2 submarines

ADVANCE (Submarine) FORCE (6th Fleet) -- VADM Teruhisa Komatsu
CL Katori (flagship, Katori) at Kwajalein
SubRon 3 -- RADM Chimaki Kono
Rio de Janeiro Maru (submarine tender, flagship) at Kwajalein
SubDiv 19 -- 4 submarines
SubDiv 30 -- 3 submarines
SubDiv 13 -- 3 submarines

SHORE BASED AIR PATROL (11th Air Fleet) -- VADM Nishizo Tsukahara
Midway Expeditionary Force -- Capt. Chisato Morita 36 Zero fighters (aboard Nagumo's carriers) 10 land-based bombers at Wake; 6 flying boats at Jaluit
24th Air Flotilla -- RADM Minoru Maeda at Kwajalein
Chitose Air Group -- 36 Zero fighters, 36 torpedo bombers at Kwajalein
1st Air Group -- 36 Zero fighters, 36 torpedo bombers at Aur and Wotje
14th Air Group -- 18 flying boats at Jaluit and Wotje