Natural antisense transcript (NAT),one prominent and complex class of regulatory RNA,is subject to regulation in stress response.In our study,strand-specific transcriptome sequencing was applied to identify 1296 sense and antisense transcripts pairs (NAT pairs) in two different drought sensitivity maize inbred lines under well water and water stressed conditions with sample-specific manner.By comparison of sense and antisense transcripts expressions,sense transcript showed higher expression level in 62.47 ％of the NAT pairs.A reciprocal inhibition expression pattern was observed between their expression and an expression balance was revealed in different antisense expression level.Epigenetic regulation of NAT pairs in drought response were investigated by comprehensive analysis of whole-genome DNA methylation profiling and small RNA sequencing.