Background The Zebu cattle are represented by a diverse group of breeds in México. Traditionally these breeds have been associated with the tough beef characteristic. Validated genetic markers have the potential to be included in marker-assisted selection and management programs in order to improve traits such as beef tenderness. The incidence and distribution of Calpain and Calpastatin polymorphisms strongly associated with beef tenderness were estimated in registered cattle of five Zebu breeds in Mexico. Results A low and in some cases null frequency of favorable C allele of CAPN316 was determined in all breeds. Conversely, a more equilibrated frequency in CAPN4751 and CAST loci was observed. Conclusions Although the relatively low occurrence of favorable alleles in assessed loci may limit their use in selection programs, genotyping availability might be a practical and comprehensive tool for introgression programs by marker assisted selection and management as to improve meat tenderness of Zebu breeds.