The insect male accessory glands/ejaculatory duct (MAG/ED) are important tissues of the male reproductive system. The MAG/ED's functions in reproduction have been well studied in Drosophila (Diptera: Drosophilidae) but remain largely unknown in the important agricultural pest Bactrocera dorsalis (Hendel) (Diptera: Tephritidae). In the present study, we re-assembled the transcriptome datasets of B. dorsalis's fat body, testis, and MAG/ED and compared these tissue-specific transcriptomes. Clean reads from these transcriptome data sets were de novo re-assembled and clustered into 31,782 unigenes (average 922 bp). In total, 21,306 unigenes were functionally annotated by Blasting against online databases. Comparative transcriptomic analysis identified numerous genes that were identified with the expressed tissue-bias patterns. Some MAG/ED-specific genes potentially involved in spermatozoa motility and capacitation (e.g., perlucin, glucose dehydrogenase, lipase), mating regulation (pheromone-binding protein—related protein), and immunity (lectin) were identified in B. dorsalis. The expressions of some of these genes were further validated by realtime quantitative polymerase chain reaction at transcriptional level. All of these identifications will help us to explore the physiological regulation of mating and reproduction in B. dorsalis in the future.