Citrus fruits are very popular food products. There are many species and varieties of them. There are also documented cases of some citrus fruits causing a severe allergic reaction. Some species of the citrus fruits, especially hybrid ones show a reduced allergenic effect due to the lack of seeds. There is a need for rapid methods for evaluation of citrus’ botanical origin. During research, the headspace of three citrus fruits Citrus Aurantifolia, Citrus japonica, and Citrus × floridana was analysed using electronic nose based on ultrafast gas chromatography and gas chromatography with mass spectrometry. In the paper, two approaches were compared. The usefulness of an electronic nose to control the quality of hybrids was demonstrated. The results obtained during ultrafast gas chromatography analyses were subjected to statistical analysis. Four chemometric methods namely: principal component analysis (PCA), discriminant function analysis (DFA), soft independent modeling of class analogies (SIMCA), statistical quality control (SQC) were used to distinguish between limequat and its parent fruits. Electronic nose combined with chemometrics is a novel analytical tool for hybrid fruits’ classification due to their botanical origin. It can supplement established techniques by providing results in a short time and at a low cost.Graphical abstract