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Anaerobic digestion is considered as a promising method to manage animal waste with antibiotic-resistant bacteria. Current research was conducted to investigate the survival of multidrug-resistant bacteria (MDRB) resistant to three groups of antibiotics: (i) cefazolin, neomycin, vancomycin, kanamycin (group 1); (ii) penicillin, oxytetracycline, ampicillin, streptomycin (group 2); and (iii) cefazolin, neomycin, vancomycin, kanamycin, penicillin, oxytetracycline, ampicillin, streptomycin (group 3), in anaerobic digestion of dairy manure and co-digestion of dairy manure and waste milk at 37°C and 55°C for 22 days, respectively. The population densities of three groups of MDRB on peptone, tryptone, yeast and glucose agar plates incubated at 30°C for 7 days before and after digestion showed 100% destruction in both digestates at thermophilic temperature. Overall reduction of more than 90% of three groups of MDRB was observed in mesophilic digestion with no significant differences (P > 0.05) between manure and milk mixture. Co-digestion of dairy manure and waste milk always produced significantly (P < 0.05) higher total gas and methane gas than digestion of manure alone at both temperatures. Gas production in each case was significantly (P < 0.05) higher in thermophilic digestion than in mesophilic digestion. The results demonstrate that thermophilic co-digestion of dairy manure and waste milk offers more benefits in terms of the environment and economy.