Whole transcriptome sequencing (RNA-seq) technologies were used to profile gene expression in dissected Arabidopsis stage 5-7 anthers and isolated male meiocytes. Previously, we reported the discovery of over 1,000 coding genes that were specifically expressed in meiocytes, some 50 genes on a large mitochondrial genome insertion on chromosome-2 pericentromeric region, and 1036 transposable element genes were up-regulated in isolated male meiocytes in comparison to the anthers. Here we present the secondary data analysis, focusing on genes that were preferentially expressed in anthers, which are likely up-regulated in anther wall cells. To assess differential expression between isolated male meiocytes and stage 5-7 anthers undergoing meiosis, we performed a negative binomial test in DESeq on the 25,881 genes expressed at a minimum of 5 reads per million in at least one sample; we identified 490 genes differentially expressed (adjusted p-value of 0.001) that had 4-fold greater expression in anthers versus meiocytes, 2 of which were only expressed in anthers. 88 genes (18%) encode unknown proteins; 27 genes are annotated coding transcription factors. In addition, well-studied anther-wall specific genes such as DYT1 (At4G21330) and ATA1 (At3G42960) are presented in this gene list. The results have advanced our understanding on the transcriptome landscapes of anthers that undergo meiosis.