There are actually quite a few biblical allusions and allegories in Lord of the Flies. Some are more obvious and more developed than others but it is not difficult to spot them.
One of the most developed and interesting is that of Simon as a Christ figure. He is given a number of characteristics including a kindness to the younger boys and an ability to go between groups without prejudice. He also begins to see and understand what is happening when none of the other boys can. He has prophetic visions and actually comes to share his understanding with the boys, but he is eventually killed. This can be interpreted as him dying for their sins and their descent into violence.
Golding suggested that perhaps the two sides of the island represent damnation and salvation. He then goes on through the action and implication of the novel to suggest that mankind will never reach salvation, that they will be stuck on the dark side (Castle Rock) of the island.
One can also look at the relationship between Jack and Ralph as mirroring that of Cain and Abel. Jack gets jealous because the boys like Ralph better and so, in the end, resolves to kill him.
There are other physical references that can be interpreted as allusions as well. The creepers being "snake things" and representing Satan and the dark side of humanity. The island itself can be interpreted as being the Garden of Eden.