Many Viburnum species are popular ornamental shrubs and, simultaneously, highly valued medicinal plants as a source of many bioactive compounds, including antioxidants. Viburnum bark, flowers, and fruits are widely used in traditional and folk medicine, and the fruits of some species are used as cooking ingredients. The knowledge of the microstructure of Viburnum fruits and the accumulation sites of bioactive substances in these organs is rather poor. Comparative analyses of the microstructure of ripe Viburnum opulus and Viburnum lantana drupes were carried out using light, scanning, and transmission electron microscopes. The location of various groups of metabolites in the fruits of both species was determined with the use of histochemical tests and fluorescence microscopy. Additionally, the major antioxidants, i.e. carotenoids, polyphenols, and flavonoids, were quantified and a number of morphometric traits of the drupes were presented. The V. opulus and V. lantana fruits were found to differ in some morphological traits and in many characteristics of the pericarp anatomy and ultrastructure. It was shown that the Viburnum fruits contained lipids and lipid compounds (carotenoids, essential oils, steroids, and saponins), polyphenols (tannins, flavonoids, and anthocyanins), pectins, and proteins. The fruits of V. opulus contained greater quantities of carotenoids, polyphenols, flavonoids, steroids, and pectins than the V. lantana drupes, whereas the latter were characterised by higher contents of essential oils, saponins, and proteins. The metabolites were located in different pericarp layers, but the greatest amounts were identified in the drupe skin.