The short regions flanked by divergent genes provide a good opportunity for exploring mechanisms of transcriptional regulation because of the confined nature of the upstream regulatory elements of both genes. We performed a genome-wide analysis of coexpression levels of divergent gene pairs in Arabidopsis thaliana, along with convergent and parallel gene pairs as controls for comparison, and found that for adjacent genes ≤0.4 kb apart, there was a significantly higher portion of gene pairs showing coexpression in divergent configuration than in parallel or convergent configuration. We divided the different expression patterns in adjacent divergent Arabidopsis gene pairs into three categories: coexpression, independent expression, and antiexpression. Our studies on the relationship between coexpression and gene function indicate that similar functionality is not the main cause for the existence of coexpressed divergent gene pairs in Arabidopsis. Comparative analysis revealed some conserved intergenic regions flanked by divergent genes ≤0.4 kb apart between Arabidopsis and rice. Additionally, we identified overrepresented motifs in the intergenic regions flanked by independently-expressed divergent genes, as compared with the intergenic sequences flanked by coexpressed divergent genes. Our analysis suggests that specific intergenic regions contain potential bidirectional promoters or genetic insulators, offering guidance for future experimental efforts to isolate those regulatory elements.