The structure and organization of the genome of Agave is still unknown. To provide a genomic tool for searching sequences of the genus, we built and characterized a binary (BIBAC2) genomic library of Agave tequilana Weber var. azul. Clones of the library had an average insert size of 170 Kb. The frequency of inserts with internal Not I sites was 30% and only 5% of the library showed organelle contamination. The library was assessed using probes with high homology to repeated regions (retroelements and rDNA regions), genes involved in the resistance to diseases (NBS-LRR) and genes related to late embryogenesis (LEA). Recombinant clones that hybridized with each of the probes were identified. Our results indicate that the obtained genomic library is suitable for the identification of sequences of interest, for genetic mapping and for studies of gene regulation and expression.