The fruits of several species of the Aronia genus were studied in the content of anthocyanins and chlorogenic acids. It was found that errors in determining the Aronia species can be excluded by using quantitative ratios between the main anthocyanins—cyanidin-3-galactoside (Cy3Gala, the main component), cyanidin-3-arabinoside (Cy3Ara), cyanidin-3-glucoside (Cy3Glu) and cyanidin-3-xyloside (Cy3Xyl). The highest level of anthocyanin accumulation was found for Aronia melanocarpa (Michx.) Elliott fruits. Meanwhile for the species differentiation the least accumulation in fruits of Cy3Glu (no more than 0.8% of the total anthocyanins) and Cy3Xyl (not more than 1.5 mol % of the amount of anthocyanins) may explored in comparison with that of A. prunifolia (Marshall) Rehder and A. mitschurinii A.K. Skvortsov & Maitul., the latter being often mistaken for black chokeberry. Even more reliable for the differentiation is the content and ratio of isomeric chlorogenic acids in the fruits. So, fruits of A. melanocarpa accumulate as the main chlorogenic acid 3-caffeoylquinic acid (3CQA, about 69.4 mol % of the sum of chlorogenic acids) and, in smaller but comparable amounts 5-caffeoylquinic (5CQA) and 4-caffeoylquinic (4CQA) acids, which account for about 14 mol %. In fruits of other species of chokeberry accumulation levels of 3CQA and 5CQA are comparable, but may vary with the change of the dominant one, while the accumulation 4CQA is characteristically low (less than 3.5 mol %). The paper discusses and experimentally confirms some errors in the sample preparation of Aronia fruit samples before the qualitative and quantitative determination of anthocyanins, and proposes a method of excluding them.