We investigated the prevalence of qnr and aac(6')-Ib-cr genes in environmental bacteria from surface water of 10 locations in Hangzhou and in clinical isolates of Enterobacteriaceae, from hospitals in four cities in China. qnrA, qnrB, qnrS, and aac(6’)-Ib-cr genes were screened using PCR, and the genotypes were analyzed by sequencing. Ten of the 78 gram-negative bacilli from water samples were C. freundii with 80% carrying the qnrB gene. qnrS1 and aac(6’)-Ib-cr genes were detected in two E. coli isolates and qnrS2 was detected in an A. punctata. The qnr and aac(6’)-Ib-cr genes were present in 72.8% and 11.6% of 103 clinical isolates of C. freundii, respectively. Of the qnr positive clinical C. freundii isolates, 65 carried qnrB, but only three and one carried qnrA1 and qnrS2, respectively, while five isolates carried both qnrA1 and qnrB, and one isolate carried both qnrS1 and qnrB. The qnrB9 gene was the dominant subtype, followed by qnrB8 and qnrB6. Southern hybridization indicated that the qnr genes are located on different plasmids. The plasmids from both environmental and clinical C. freundii isolates appeared to be homogenous