Pseudomonas aeruginosa is a serious nosocomial pathogen with high morbidity and mortality due to the increasing resistance to antibiotics in recent years. qnrVC genes have been proven as a source of antibiotic resistance, but relationship with Pseudomonas aeruginosa remains not clear. We aimed to investigate the prevalence and molecular characteristics of qnrVC genes in P. aeruginosa clinical isolates. A total of 874 nonduplicate clinical isolates were collected in Guangdong, China, between January 2011 and June 2015. The presence of qnrVC genes and their genotypes were determined using PCR amplification and DNA sequencing. Antibiotic susceptibilities were tested, and the genetic relatedness of qnrVC-positive isolates were analyzed by multi-locus sequence typing (MLST) and pulsed field gel electrophoresis (PFGE). Consequently, we found 2.3% of P. aeruginosa isolates were present with qnrVC genes, displaying more resistant to various antibiotics. Phylogenetic analysis of qnrVC-positive strains revealed that antibacterial resistance among qnrVC-positive P. aeruginosa isolates in Guangdong probably emerged from multiple sources and was not spread by clonal strains.