Bitterness in almonds is controlled by a single gene (Sk dominant for sweet kernel, sk recessive for bitter kernel) and the proportions of the offspring genotypes (SkSk, Sksk, sksk) depend on the progenitors’ genotype. Currently, the latter is deduced after crossing by recording the phenotype of their descendants through kernel tasting. Chemical markers to early identify parental genotypes related to bitter traits can significantly enhance the efficiency of almond breeding programs. On this basis, volatile metabolites related to almond bitterness were investigated by Solid Phase Microextraction-Gas Chromatography-Mass Spectrometry coupled to univariate and multivariate statistics on 244 homo- and heterozygous samples from 42 different cultivars. This study evidenced the association between sweet almonds’ genotype and some volatile metabolites, in particular benzaldehyde, and provided for the first time chemical markers to discriminate between homo- and heterozygous sweet almond genotypes. Furthermore, a multivariate approach based on independent variables was developed to increase the reliability of almond classification. The Partial Least Square-Discriminant Analysis classification model built with selected volatile metabolites that showed discrimination capacity allowed a 98.0% correct classification. The metabolites identified, in particular benzaldehyde, become suitable markers for the early genotype identification in almonds, while a DNA molecular marker is not yet available.