Our previous studies have shown that tCUP, a cryptic promoter from tobacco, functions in all living plant cell types in a wide range of plant species. This led us to investigate if an enhanced derivative, EntCUP Δ, could be used to drive the neomycin phosphotransferase II (nptII) gene and select for kanamycin resistance in crop species that regenerate by organogenesis or embryogenesis. Tobacco (leaves), cauliflower (hypocotyls) and alfalfa (leaves, petioles, stems) explants were co-cultivated with Agrobacterium containing either EntCUP Δ -nptII-nos or 35S-nptII-nos to compare the efficiency of selection for kanamycin resistance. The infected alfalfa explants were placed in somatic embryo induction media, whereas tobacco and cauliflower explants were placed in shoot induction media with kanamycin at concentrations that normally inhibit regeneration. Transgenic plants were recovered from all of the explants with both selectable marker gene constructs. The transformation efficiencies using tCUP Δ -nptII-nos were comparable to or higher than those using 35S-nptII-nos in all three species tested. This study demonstrated that promoters which are not associated with expressed plant genes can be used as alternatives for the expression of selectable marker genes in a broad range of tissues and species for the generation of transgenic plants.