The anthers in flowers perform important functions in sexual reproduction.Seldom studies have been made to study anther transcriptomes to explore genes controlling anther development.To analyze the characteristics ofgene expression during the male sterile anther degeneration, we produced transcriptomes of anthers of radish (Raphanus sativus L.) at three progressive developmental stages with cDNA-AFLP.The transcriptomes included at least 2556 unique transcripts, which involved in transcription, signal transduction, DNA synthesis, cell growth and others.The differential developmental profiles of the transcripts signify extensive regulation of gene expression in the anther during development.The transcriptomes were used to dissect the major abnormality of gene expression of the sterile anther.First, we categorized and charted the developmental profiles of all transcripts present in the anther;, the transcripts of the sterile anther represent obviously difference contrast to the fertile anther.Second, we successfully selected from hundreds of transcripts encoding proteins for transcription, signal transduction, materials transport, and pollen wall formation.The results suggested that male sterile mutant disrupted pathways during microspore development in which the cells were undergoing rapid reorganization and are transforming into more specialized cell types, and implied that cytoplasmic male sterile mutant might affect an anther developmental pathway with a few genes expressed in tapetum cells which block the materials transport to the microspore, which further leads to the disordered expression of a large number of genes involved in transcription, signaling pathways, microspore or pollen wall formation, and materials transport in pollen grains.