Multidrug-resistant (MDR) Enterobacteriaceae critically threaten duck farming and public health. The phenotypes, genotypes, and associated mobile genetic elements (MGEs) of MDR Enterobacteriaceae isolated from 6 duck farms in Zhejiang Province, China, were investigated. A total of 215 isolates were identified as Escherichia coli (64.65%), Klebsiella pneumoniae (12.09%), Proteus mirabilis (10.23%), Salmonella (8.84%), and Enterobacter cloacae (4.19%). Meanwhile, all isolates were resistant to at least two antibiotics. Most isolates carried tet(A) (85.12%), blaTEM (78.60%) and sul1 (67.44%) resistance genes. Gene co-occurrence analysis showed that the resistance genes were associated with IS26 and integrons. A conjugative IncFII plasmid pSDM004 containing all the above MGEs was detected in Proteus mirabilis isolate SDM004. This isolate was resistant to 18 antibiotics and carried the blaNDM-5 gene. MGEs, especially plasmids, are the primary antibiotic resistance gene transmission route in duck farms. These findings provide a theoretical basis for the rational use of antibiotics in farms which are substantial for evaluating public health and food safety.