This novel comparative study tended to disclose how the molecular structures present in seven azo dyes including two types of azo dyes (i.e., naphthol type azo dyes--Reactive Black 5 (RB 5), Reactive Blue 171 (RB 171), Reactive Green 19 (RG19), Reactive Red 198 (RR198), Reactive Red 141 (RR141), and non-naphthol type azo dyes--Direct Yellow 86 (DY86), Reactive Yellow 84 (RY84)) affected color removal capability of Aeromonas hydrophila. Generally speaking, the decolorization rate of naphthol type azo dye with hydroxyl group at ortho to azo bond was faster than that of non-naphthol type azo dye without hydroxyl group, except of RG19. The azo dyes with electron-withdrawing groups (e.g., sulfo group in RR198, RB5 and RR141) would be easier to be decolorized than the azo dyes with the electron-releasing groups (e.g., -NH-triazine in RB171 and RG19). In addition, the azo dyes containing more electron-withdrawing groups (e.g., RR198, RB5 and RR141) showed significantly faster rate of decolorization. The azo dyes with electron-withdrawing groups (e.g., sulfo group) at para and ortho to azo bond (e.g., RR198, RB5 and RR141) could be more preferred for color removal than those at meta (e.g., DY86 and RY84). The former azo dyes with para and ortho sulfo group provided more effective resonance effects to withdraw electrons from azo bond, causing azo dyes to be highly electrophilic for faster rates of reductive biodecolorization. However, since the ortho substituent caused steric hindrance near azo linkage(s), azo dyes with para substituent could be more favorable (e.g., SO(2)(CH(2))(2)SO(4)(-) in RR198 and RB5) than those with ortho substituent (e.g., sulfo group at RR141) for decolorization. Thus, the ranking of the position for the electron-withdrawing substituent in azo dyes to escalate decolorization was para>ortho>meta. This study suggested that both the positions of substituents on the aromatic ring and the electronic characteristics of substituents in azo dyes all significantly affected the performance of biodecolorization of A. hydrophila.