This study assesses the performance of an aerobic trickling filter, down-flow hanging sponge (DHS) reactor, as a decentralized domestic wastewater treatment technology. Also, the characteristic eukaryotic community structure in DHS reactor was investigated. Long-term operation of a DHS reactor for direct treatment of domestic wastewater (COD = 150–170 mg/L and BOD = 60–90 mg/L) was performed under the average ambient temperature ranged from 28°C to 31°C in Bangkok, Thailand. Throughout the evaluation period of 550 days, the DHS reactor at a hydraulic retention time of 3 h showed better performance than the existing oxidation ditch process in the removal of organic carbon (COD removal rate = 80–83% and BOD removal rate = 91%), nitrogen compounds (total nitrogen removal rate = 45–51% and NH4 +–N removal rate = 95–98%), and low excess sludge production (0.04 gTS/gCOD removed). The clone library based on the 18S ribosomal ribonucleic acid gene sequence revealed that phylogenetic diversity of 18S rRNA gene in the DHS reactor was higher than that of the present oxidation ditch process. Furthermore, the DHS reactor also demonstrated sufficient COD and NH4 +–N removal efficiency under flow rate fluctuation conditions that simulates a small-scale treatment facility. The results show that a DHS reactor could be applied as a decentralized domestic wastewater treatment technology in tropical regions such as Bangkok, Thailand.