Iris dichotoma with different flower colors and I. domestica are beardless wild irises belonging to the family Iridaceae that bloom in the summer and have long flowering periods. In this study, we collected three accessions of I. dichotoma with violet, yellow, and white flowers, respectively, in China, and crossed them with I. domestica individuals. The flower color of the hybrids derived from these crosses was categorized into eight groups: violet, purple, brown, orange, red, pink, yellow, and white. From this population, 45 individuals were selected for analysis, and their fully expanded inner and outer perianths were harvested for extraction of anthocyanins. Using high-performance liquid chromatography-mass spectrometry (HPLC-MS) analysis, 29 anthocyanins were identified by comparing MS and UV-visible spectra and elution order based on published data and guidelines. The 29 anthocyanins were classified into six groups: non-acylated glycosides (3RG, 3RG5G), acetylglycosides (3acRG5G), p-coumaroylglycosides (3pCRG, 3pCRG5G), caffeoylglycosides (3CRG5G), feruloylglycosides (3feRG, 3feRG5G), and acetyl-(p-coumaroyl) glycosides (3ac-pCRG5G). Acylated anthocyanin contents were considerably higher than non-acylated anthocyanin contents in the individuals evaluated, regardless of flower color, except in the yellow-flowered I. dichotoma and its yellow-flowered progeny. We found ten anthocyanins derived from pelargonidin, including pelargonidin 3-O-(caffeoyl)rutinoside-5-O-glucoside (Pg3CRG5G), pelargonidin 3-O-(feruloyl)rutinoside-5-O-glucoside (Pg3feRG5G), and pelargonidin 3-O-(feruloyl)rutinoside (Pg3feRG), that have not yet been reported in other Iris species. Moreover, delphinidin 3-O-(feruloyl) rutinoside-5-O-glucoside (Dp3feRG5G), and delphinidin 3-O-(feruloyl)rutinoside (Dp3feRG) were also characterized for the first time in Iris. Two to five major anthocyanins were detected in the petals of the violet and purple groups, whereas those of the brown group contained three to six anthocyanins. Petals of the orange, red, and pink groups contained two to four major anthocyanins. The total variance explained by the first two principal components (PC) in a PC analysis of the intensities of the compound peaks detected in individuals representing the eight color groups was 44.7%. Individuals were classified into 10 types (A-I to A-X) according to their anthocyanidin composition in the flower petals. Knowledge of the types of anthocyanins determining flower petal color will aid comprehensive understanding of flower color characteristics in hybrid progeny and will contribute to the development of breeding Iris cultivars of diverse flower colors.