A rational generic concept in the group of Prunus sensu latissimo (Rosaceae) remains debatable, with two main approaches or traditions: one favouring a broad circumscription of Prunus, and another preferring its splitting into numerous segregate genera such as Armeniaca, Cerasus, Emplectocladus, Laurocerasus, Maddenia, Padus, Persica, Prunus s. str., Pygeum, etc. Members of these groups often hybridise with each other to form intermediates. This situation is parallel to the taxonomic options in another group of Rosaceae, the tribe Maleae, in which some authors recognise numerous genera (Aria, Aronia, Chaenomeles, Cotoneaster, Cydonia, Eriobotrya, Malus, Photinia, Sorbus, etc.). In contrast, others prefer a mega-genus Pyrus sensu latissimo. The genus Amygdalus (as well as other segregated genera mentioned above) is not recognised by many researchers and is considered a part of the genus Prunus s. l. However, species usually placed in Amygdalus are quite peculiar and habitually differ from other “prunoid” genera. The main feature distinguishing Amygdalus from closely related genera is the dry pericarp that opens when ripe. The group described as the section Chamaeamygdalus is the most isolated in Amygdalus. It includes low thornless shrubs with narrow leaves and small, densely tomentose-shaggy fruits. The shape of the calyx tube is a morphological feature that distinguishes the species of the section Chamaeamygdalus from the typical section of the genus. Phylogenetic analyses based on molecular data confirm the morphological differences between species of the section Chamaeamygdalus, which is the basis for assigning the generic rank to this group. The new genus Chamaeamygdalus is erected here, and three new species-rank nomenclatural combinations are validated for species of this genus.