In Arteaga, Coahuila, Mexico, different apple mutants derived from the Golden Delicious cultivar have been identified. They are characterized by their low chilling requirements (350–650 Chilling units (CU)) for breaking dormancy, and high flower production. The aim of this study was to determine the bromatological, genetic, and DNA methylation differences among ten apple mutants, and the wild-type Golden Delicious cultivar. The bromatological analyses showed that there are slight differences between some apple mutants with respect to control (Golden Delicious); in most cases, mutants were similar to each other. On the other hand, the genetic diversity among apple genotypes accessed by ISSR markers showed 57.12% of polymorphism among the 11 apple genotypes. The methylation assay showed that the Verde mutant from the Huachichil location had the highest values of DNA methylation (87.49%), even higher than the control (Golden Delicious). Furthermore, in the San Antonio of Alazanas location, the Tunal and Vigas II mutants showed the highest values of DNA methylation (62.85 and 87.61, respectively), however, the chilling requirements between these two cultivars are very different (340 and 750 CU, respectively), so it was concluded that a higher chilling requirement, is not always caused by a higher percentage of methylation. The study of these mutants may allow development of apple tree cultivars with desirable characteristics under warm winter conditions. •Characterization of apple trees with a low requirement for cold hours.