Kojiki
Almost all the myths that are still surviving came from this book.
Read a preview on Google Books.
Kotoamatsukami
These are the first stories appearing at the time of the creation of the universe.
After the creation of the universe, there was Kamiyoyano, which was the emergance of seven generation of gods after the Earth and and Heaven came into being.
The first two generations were individual gods, and the next five were pairs of brother and sister gods who were also married. In the Kojiki, there were 12 deities that made the Kamiyoyano.
Influence
Buddhist and Shinto beliefs heavily dictate Japanese myths, since they are the 2 main religions practiced in Japan.
Nihon Shoki
This is another set of books that states that rather than emerging after the Earth and Heaven, the Kamiyoyano came after the Universe was created.
It also says that the first three generations were single deities, and the rest came to be as couples.
Izanagi and Izanami
After the gods came from the splitting of the Earth and the Heaven, the older gods ordered Izanagi and Izanami to create the islands of Japan. Izanagi and Izanami then went to the floating bridge of heaven, and churrned the primeval ocean with a heavenly spear. From the drops of the spear, the island Onogoro was formed. Izanagi and Izanami then went their to marry. They performed the ritual and got married, but their first child was deformed. The error was that Izanami, a woman, spoke first. Izanagi and Izanami performed the ritual again, this time, Izanagi spoke first. Then they gave birth to eight children, who became the islands of Japan. They then started giving birth to many other gods that represented aspects of nature, but when Izanami gave birth to Kurotsuchi, the god of fire, she got a terrible burn and started dying. She was still giving birth to other gods too, while she was dying. Izanagi was enraged after his wife's death and killed Kurotsuchi, of whose blood emerged even more gods. Izanagi then decided to go to Yomi, the land of the dead, to bring his wife back. It was very dark there, and when he reached Izanami, she explained that she couldn't leave after eating the food there, but still made arrangements to leave. She did warn Izanagi to not look at here. Izanagi was so anxious about seeing his wife, that he lit a torch to see her. He was horrified at the sight of a rotting corpse instead of his wife, and Izanami was furious that Izanagi betrayed her wishes. Izanami then sent many hideous female spirits and thunder gods to catch Izanagi. Izanagi escaped them, and Izanami herself. When he reached the land of the living, he moved a giant boulder, which block the passageway between the worlds. Izanami cursed that she will cause the death of 1,000 people per day. Izanagi countered this by saying that he would give birth to 1,500 people per day. Izanagi and Izanami then divorced. Izanagi then felt unclean, and took a bath to purify himself. Gods both good and evil emerged from his discarded appendages, and three major gods appeared when he washed his face. Amaterasu, goddess of the sun, was born from his left eye, Tsukiyomu, god of the moon, was born from his right eye, and Susano-o, the god of storms, was born from his nose. Izanagi was very proud of his noble children and divided his kingdom up among them.
Amaterasu and Susano-o
Susano-o was very unhappy with his share of the world and caused a lot of destruction and choas. Because of this, he was banished to Yomi. Susano-o was very clever, and asked to see his sister one last time. Amaterasu knew that he was plotting something, so they decided to have a contest of power. If Susano-o wins, he got to stay in heaven, but he would get sent back to Yomi if he lost. Amaterasu took Susano-o's sword, broke it into three pieces, and chewed it. When she spat it out, three goddess emerged. Susano-o then took five star shaped beads from Amaterasu's necklace and started chewing them. When he spat them out, five gods emerged. Amaterasu pointed out that Susano-o used her power to produce five gods, so she technically won, but she still allowed Susano-o to stay. Susano-o immediately started causing trouble again. He violated many rules, such as destroying rice crops, making loud noises, and dirtied the floor of Amaterasu's palace. He went too far when he took one of the horses in heaven, skinned it, and threw it into the hall where Amaterasu was weaving cloth. Amaterasu could not take it any longer, and went to hide in a cave. This caused the world to be plunged into darkness, and the other gods started to worry. The tried to do many things to get Amaterasu to get out, but they weren't working. The other gods started acting like they were having a great time and starting having fun. Amaterasu wondered how they could be having so much fun without her, and slightly opened the entrace to the cave. The other gods replied that there was a god more brilliant than her. Amaterasu was suprised by this and wanted to see who this god was. The other gods got a mirror, and Amaterasu was so interested in the reflection's brilliance that started walking out of the cave. Then the gods sealed the entrance to the cave, and banished Susano-o. All was back to normal.