Citrus taxonomy is confusing with several discordant classification systems. It results from the reticulate evolution of the cultivated citrus combining speciation process during allopatric evolution and further interspecific hybridizations at the origin of most citrus cultivars with interspecific mosaic genomes fixed by apomixis. This citrus evolution generated a lot of chemical and phenotypic diversity. The citrus essential oils are complex mixture of hundred aromatic compounds. The taxa specific compounds are rare and sometimes misleading in determining the taxonomic position of a citrus fruit. It is preferable to consider for classification the proportion of major compounds rather than the absence or presence of minor compounds. For example, the approximate proportions of limonene (35%), geranial (20%) and neral (15%) characterize the peel essential oil (PEO) of C. medica. The profile of myrcene (30%) and neryl acetate (25%) is specific to the leaf essential oil of P. trifoliata. Nevertheless chemotaxonomy has limitations in terms of effectiveness that can be verified by the presence of compounds in the genealogies that are absent in the parents essential oils. Sometimes some compounds are shared by two citrus taxa without any phylogenetic relationship between them. This is the case of β-pinene present in high proportion in C. halimii PEO as in C. maxima varieties while the genetic markers concluded to a phylogenic relation with Fortunella species. The use of genetic markers and more specifically those that can detect the ancestral species (SNP diagnostic) is much more efficient than the comparison of secondary metabolites to resolve the taxonomic misunderstanding and the classification of unknown citrus hybrids. The main difficulty in citrus classification lies in the representativeness of a species to define the specificity of an aromatic compound or even of a diagnostic genetic marker.