This topic has been discussed on the enotes page listed below. However, here is a quick summary.
The main theme is the battle between good and evil. The battle can be between good vs. evil people or it can be a fight in the life of one person as they decide what choices they will make in life. This battle is seen in the biblical story of Cain and Abel, and it was shown again when Steinbeck has Lee explain the story of Cain ad Abel to Samuel and Adam. This theme later carries on through the character of Caleb. (In addition to the good versus evil question of the Cain and Abel story, there is also a question of sibling rivalry which is furthered in the lives of Charles and Adam, as well as Cal and Aron.
Although good vs. evil is the main theme, there are also minor ones found throughout the novel. There is the concept of timshel, which translates as “thou mayest” and teaches that we don’t have to be influenced by our dark family histories. The theme of truth is discussed, as well as fatherhood and the question of whether the sins of the father are really to be visited upon the son, as the Bible states in Psalms 79:8.