Integrated fish farming is commonly practiced in Guangdong Province in South China. Animal manure generated from livestock and poultry (commonly pigs and ducks) is directly excreted into, or transported via pipes, to fish ponds where the nutrients support the growth of photosynthetic organisms. The use of a wide variety of antimicrobials in livestock and poultry has led to antimicrobial-resistant bacteria. Thus, there is concern over the potential for transfer of these bacteria into the integrated culture systems. Our objective was to determine the antimicrobial susceptibility and homology of were isolated from pig/duck waste, fish, pond water, and sediments from four integrated fish farms in Guangdong Province. We used the Kirby-Bauer disk diffusion method to determine the susceptibilities to 8 classes of 24 antimicrobials. The genomic DNA of the isolates was extracted and the molecular typing was analyzed by entero bacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR) and pulsed field gel electrophoresis (PFGE).The resistance frequencies of ampicillin, amoxicillin/clavulanate, and rifampicin were relatively high in the 57 isolates, and the resistance profiles varied among the different isolates. The isolates were grouped into 24 clusters by ERIC-PCR and 46 clusters by PFGE. Isolates from different sources within the same integrated fish farm exhibited similar or identical genotyping patterns between the two molecular typing methods, and they were also associated with similar resistance patterns suggesting they were homologous. Our results suggest that ERIC-PCR and PFGE have use for analysis of clonal relationships and tracing of the source of resistance in Integrated fish farming systems appear to be susceptible to the transfer of drug-resistant bacterial strains from livestock and poultry to fish or the environment. The impact of antimicrobial resistance in the fish was not addressed in this study and remains to be determined.