How to draw the boxplot with significant level?

I know that this is an old question and the answer by DatamineR already provides one solution for the problem. But I recently created a ggplot-extension that simplifies the whole process of adding significance bars: ggsignif

Instead of tediously adding the geom_line and annotate to your plot you just add a single layer geom_signif:

library(ggplot2)
library(ggsignif)

ggplot(iris, aes(x=Species, y=Sepal.Length)) + 
  geom_boxplot() +
  geom_signif(comparisons = list(c("versicolor", "virginica")), 
              map_signif_level=TRUE)

Full documentation of the package is available at CRAN.