Certain aromatic amines generated by the decolorization of some azo dyes are not removed substantially by conventional anaerobic-aerobic biotreatment. These aromatic amines are potentially toxic and often released in the wastewater of industrial plants. In this study, the fate and transformation of the naphthylaminesulfonic azo dye Reactive Black 5 (RB5) during different phases of a sequencing batch reactor were investigated. The major products of RB5 decolorization during the anaerobic phase include 2-[(4-aminophenyl)sulfonyl]ethyl hydrogen sulfate (APSEHS) and 1-2-7-triamino-8-hydroxy-3-6-naphthalinedisulfate (TAHNDS). During the aerobic phase, APSEHS was hydrolyzed and produced 4-aminobenzenesulfonic acid, which was further degraded via dearomatization. TAHNDS was transformed rapidly via auto-oxidation into TAHNDSDP-1 and TAHNDSDP-2, which were not further removed by the activated sludge during the entire 30-day aerobic phase. In contrast, different behaviors of TAHNDS were observed during the anoxic phase. The transformation of TAHNDS was initiated either by deamination or desulfonation reaction. TAHNDS was then converted into 3,5-diamino-4-hydroxynaphthalene-2-sulfonic acid, which was subsequently removed via ring cleavage reaction under aerobic condition. In conclusion, complete degradation of TAHNDS by activated sludge occurs only during anoxic/aerobic processes instead of the conventional anaerobic/aerobic processes.