Atopic dermatitis (AD) is a paradigmatic inflammatory chronic skin disease. As for other chronic skin diseases, (i) the spectrum of the clinical phenotype and severity as well as (ii) the genetic background and (iii) the underlying mechanisms strongly suggest a high degree of pathophysiological heterogeneity yet leading to a similar clinical pattern, that is, the eczematous skin lesion, but showing distinct progression patterns. This review suggests to exploit the recent knowledge about AD for a novel approach proposing a tentative first molecular taxonomy of this disease based on the genotype and endophenotype. The consequences in terms of personalized prevention and management are delineated.As an evolution of the biomedical research and our genetic and pathophysiological understanding of complex diseases, we are currently experiencing a new trend in the classification of diseases moving from the purely phenotypic definition to a molecular taxonomy. It is expected that in future medicine, every disease will be characterized by three main groups of information: (i) the genotype, including epigenotypic information, (ii) the endophenotype (1) that comprises all available biomarkers (BMs), and (iii) the clinical phenotype (Fig. 1). Among all chronic inflammatory diseases, atopic dermatitis (AD) represents a paradigmatic condition because of its genetic and pathophysiological complexity (2) and finally the result thereof: the wide spectrum of clinical phenotype (3). This wide spectrum includes at one end the very minor forms such as atopic stigmata or simply dry skin with minimal itching and the erythrodermic and most severe form of AD at the other end. Due to the recent progress in the research of genetic, immunologic, and environmental factors (the so-called exposome) leading to AD, we are just starting to understand the complexity of the mechanisms underlying the variety in the clinical phenotype and to make first attempts to link the genotype and endophenotype to distinct clinical forms and courses of this disease such as the atopic march. After exposing a brief update of the clinical phenotype and pathophysiological aspects, this review introduces the concept of molecular taxonomy for AD and the consequences for its future management in the context of stratified or personalized medicine.