The failure of peg penetration into the soil leads to seed abortion in peanut.Knowledge of genes involved in these processes is comparatively deficient.Here, we used RNA-seq to gain insights into transcriptomes of aerial and subterranean pods.More than 2 million transcript reads with an average length of 396 bp were generated from one aerial (AP) and two subterranean (SP1 and SP2) pod libraries using pyrosequencing technology.