Objectives To identify the prevalence of ESBL genes in the principal group of Enterobacteriaceae causing nosocomial infections and to identify the phylogenetic group in Escherichia coli isolates. Methods There were collected 1084 ESBL-producing Enterobacteriaceae isolates during 2005–2012 from adult patients from 14 hospitals and corresponding to eight states and five regions (SE, S, N, W and NW) in Mexico. The CTX-M-(CTX-M-1 group), SHV-, TLA- and GES-type ESBLs genes were screened. The respective alleles were determined in the most of ESBLs genes. In E. coli isolates selected were used to identify the phylogenetic group. Results The ESBL-producing Escherichia coli and Klebsiella pneumoniae corresponded the most prevalent clinical isolates. CTX-M-type ESBLs genes were the most common, followed by SHV-type, GES-type and the ESBLs TLA-1 gene. The allelic frequency showed to CTX-M-15 ESBL the most prevalent, followed by the SHV-12, SHV-5 and GES-1, GES-19 in the GES family. Among ESBL-producing E. coli isolates the phylogenetic groups A and D were the most common ones. Conclusions The present study showed an epidemiological change in terms of bacterial species, placing E. coli as the most frequently isolated bacteria among ESBL-producing Enterobacteriaceae in Mexico, followed by K. pneumoniae . This frequency is accompanied by a high frequency of ESBL CTX-M-15.