Objective To investigate the genotypic character of clinical isolates producing extended spectrum beta-lactamases(ESBLs). Methods ESBLs producing Escherichia coli and Klebsiella pneumoniae isolates were indentified by phenotyic confirmatory test. PCR were using to detect TEM, SHV and CTX-M genes. Results The positive rates of TEM, SHV and CTX-M genes of these isolates were 40.4%, 20.7% and 83.3% respectively. Those of Escherichia coli were 48.1%, 1.3% and 93.5% respectively. Those of Klebsiella pneumoniae were 24.3%, 81.1% and 62.2% respectively. 46.8% of Escherichia coli and 51.4% of Klebsiella pneumoniae had more than one genotype. Conclusions The major genotype of ESBLs-producing Escherichia coli was CTX-M and which of Klebsiella pneumoniae was SHV. Many isolates had more than one genotype.