The fruits of Cornus mas and Cornus officinalis have been known and appreciated in folk medicine for years and have a high biological value, which is mainly connected with their polyphenols and iridoids content. However, hybrids of C. mas × C. officinalis have not been investigated. The aim of this study was to evaluate the iridoids, anthocyanins, and flavonols content, and antioxidant capacity of Cornus mas, Cornus officinalis, and C. mas × C. officinalis. Iridoids and flavonoids were quantified by the High-Performance Liquid Chromatography (HPLC) method. Antioxidant capacity (AC) was measured using 2,2-diphenyl-1-picrylhydrazyl (DPPH•), 2,2′-azino-bis (3-ethyl benzothiazoline-6-sulfonic acid (ABTS•+), and ferric reducing antioxidant power (FRAP) tests. Total phenolic content (TPC) was evaluated using the Folin–Ciocalteu reagent. Among the C. mas cultivars and C. officinalis genotypes, there was considerable variation in the content of iridoids, flavonoids, and AC. Interspecific hybrids C. mas × C. officinalis contained more iridoids than C. mas and more anthocyanins than C. officinalis and additionally had higher AC and TPC than C. officinalis and most C. mas. AC, TPC, and the presence of iridoids, anthocyanins, and flavonols in hybrids C. mas × C. officinalis are reported for the first time. The Cornus species deserve special attention due to their highly biologically active substances, as well as useful medicinal properties.