In South Western Indian ocean (IO), Extended-Spectrum β-Lactamase producing Enterobacteriaceae (ESBL) are a main public health issue. In livestock, ESBL burden was unknown. The aim of this study was estimating the prevalence of ESBL on commercial farms in Reunion, Mayotte and Madagascar and genes involved. Secondly, risk factors of ESBL occurrence in broiler, beef cattle and pig farms were explored. In 2016-2017, commercial farms were sampled using boot swabs and samples stored at 4°C before microbiological analysis for phenotypical ESBL and gene characterization. A semi-directive questionnaire was performed. Prevalences observed in all production types and territories were elevated, except for beef cattle in Reunion which differed significantly. The most common ESBL gene was the CTX-M-1 subtype. Generalized linear models explaining ESBL occurrence varied between livestock production sectors and allowed identifying main protective (e.g., water quality control and detergent use for cleaning) and risk factors (e.g., recent antibiotic use, other farmers visiting the exploitation, pet presence). This study is the first to explore tools for antibiotic resistance management in IO farms. It provides interesting hypothesis to explore about antibiotic use in IO and ESBL transmission between pig, beef cattle and humans in Madagascar.