Recently, interspecies quorum quenching by bacterial cells has been reported as a novel approach to the biofouling control in a membrane bioreactor (MBR) for wastewater treatment. In this study, a novel quorum quenching (QQ) bacterium, Pseudomonas sp. 1A1, was isolated from lab-scale MBR and was encapsulated in a microbial vessel made of a hollow fiber microporous membrane for the biofouling control in MBR. Pseudomonas sp. 1A1 was most likely to produce AHL-acylase and degraded to a wide range of N-acyl homoserine lactones (AHLs), although there was a large difference in the degradation rate of each AHL. It has an extracellular QQ activity, i.e., it produces QQ enzymes, and excretes them out of the cell. The microbial vessel encapsulating Pseudomonas sp. 1A1 was applied to a lab-scale MBR and proved substantial inhibition of the membrane biofouling.