This research was part of a study of filamentous growth and control in an ultracompact biofilm reactor (UCBR). Morphologies of biofilm and filamentous bacteria in the UCBR were investigated. Ethanol was used as a substrate and sodium hypochlorite was applied as a toxicant to control filamentous growth. The results indicated that factors such as chemical oxygen demand, surface loading rate, pH, and dissolved oxygen could initiate filamentous overgrowth in the UCBR. Different biofilm and filamentous morphologies in the UCBR were observed under different operational conditions. Chlorination was an effective approach to control filamentous growth during and after biofilm formation. Proper chlorine dosing had no effect on biofilm, but killed filaments. Overdose of chlorine damaged biofilm and caused adverse effects such as low treatment efficiency, media clogging and washout, and biofilm color change in the reactor. Frequent monitoring of the morphologies of filaments and biofilm was needed during chlorination to prevent chlorine overdose.