Introduction: The main objective of the study was the molecular characterization of extended spectrum β-lactamases (ESBL) in Escherichia coli isolates collected from human and bovine samples in Oyo state, Nigeria. Methodology: Between August 2010-2011, 114 E. coli isolates were collected from hospitals (n = 57) and bovine (n = 57). PCR and sequencing were used for identification of ESBLs, upstream sequences, plasmid-mediated quinolone resistance (PMQR) genes and class 1 integrons. Plasmid incompatibility groups were identified among ESBL-positive isolates by PCR. Genetic relatdness was assessed by rep-PCR and MLST. Transfer of ESBL determinants to the recipient strain E. coli J53 was performed by broth mating assays. Results: CTX-M15 was the unique ESBL found in eight human isolates. Six CTX-M-15 producers also carry the aac(6')-lb-cr gene and/or qnrB gene, and class 1 integrons. FIA, FIB, H11, H12, F, Y and K were the plasmid replicon types found. CTX-M-15 and PMQR determinants were transferred by conjugation in two E. coli assigned by MLST to ST131 and ST2695, a new allele. Conclusions: The study highlights the dissemination hability of CTX-M-15 associated with PMQR, and the presence of class 1 integrons, able to capture additional genes, justifying the urgent need of antimicrobial resistance surveillance in Nigeria.