Abstract: Objectives　To explore the route of ESBL producing bacteria in neonatal faeces, and to investigate the gene and drug resistance of ESBL producing bacteria in intestinal tract of neonates. Methods　Fecal samples of healthy newborns and their mothers were collected, and bacterial cultures were carried out using selective ESBL medium. The positive strains were identified by Time-of-flight mass spectrometry. ESBL genotyping and resistance gene detection were performed by whole genome sequencing technique. Results　In 146 neonatal fecal specimens, the positive rate of ESBL producing bacteria was 8.90%,and the positive rate in the first time stool was 3.23%. Seventy-two hours after birth, the positive rate of fecal ESBL producing bacteria was 13.10%. Among the 13 ESBL producing strains, there were 9 strains of CTX type, 3 strains of TEM type and 1 strain of SHV type. Nine strains of CTX include five types such as CTX-M-24, CTX-M-18, CTX-M-27, CTX-M-42 and CTX-M-15. The positive rate of ESBL producing bacteria was 21.6% in 167 mothers' fecal specimens. The ESBL genotype included 24 strains of CTX type, 6 strains of TEM type, 4 strains of SHV type and 2 strains of QnrS type. Twenty-four strains of CTX include CTX-M-24, CTX-M-14, CTX-M-18, CTX-M-27, CTX-M-42 and CTX-M-15. There were 2 or 3 ESBL genotypes in 12 maternal and neonatal specimens. It was detected to have 6 types of resistance gene such as aadA5, strA, strB, sul1, sul2 and dfrA17 in 49 strains of ESBL producing bacteria in maternal and neonatal strains. Resistance genes were exactly the same in the neonates as in mothers who were detected to have ESBL producing bacteria. A variety of resistance genes were detected in feces in 7 neonates and 23 mothers. Conclusions The neonates in hospital may be detected to have ESBL produing bacteria in the intestinal tract at the same time as their mothers or separately. However, there are many ways for neonates to have ESBL producing bacteria in intestinal tract. There are many genotypes and resistance genes of ESBL producing bacteria.