An anaerobic sequencing batch reactor (ASBR), seeded with a biomass inoculum that previously had not been exposed to the macrolide antimicrobial tylosin (mixture of Tylosin A, B, C, and D), was operated for 3 months with swine waste without Tylosin A and for 9 months with swine waste containing Tylosin A at an average concentration of 1.6 mg/L. When swine waste with tylosin was fed to the ASBR, methane production and volatile solids removal did not appear to be inhibited and a methane yield of 0.47 L methane per gram volatile solids fed to the ASBR was observed. Throughout the operating period, Tylosin A levels in ASBR biomass and effluent were below the detection limit of 0.01 mg/L. However, during the first 3 months of operation, the levels of macrolide-lincosamide-streptogramin B (MLSB)-resistant bacteria in the ASBR biomass increased substantially as determined by hybridizations with oligonucleotide probes designed to target MLSB-resistant bacteria. Since no Tylosin A was present in the swine waste during the initial 3 months, the presence of MLSB-resistant bacteria in the swine waste was likely the reason for the increase in resistance. Subsequently, the levels of MLSB-resistant bacteria in ASBR biomass stabilized with an average of 44.9% for the 9 months of operation with swine waste containing Tylosin A. The level of MLSB-resistant bacteria in the swine waste fed to the ASBR during this period averaged 18.0%. The results indicate that anaerobic treatment of a waste stream containing tylosin was effective (based on reactor performance) and that the level of resistant bacteria in the ASBR was substantially higher than in the waste stream fed to this system.