The genus Aronia Medik., also known as chokeberry, is a group of deciduous shrubs in the Rosaceae family, subtribe Pyrinae. The four commonly accepted species include A. arbutifolia (L.) Pers., red chokeberry; A. melanocarpa (Michx.) Elliott, black chokeberry; A. prunifolia (Marshall) Reheder, purple chokeberry; and A. mitschurinii (A.K. Skvortsov & Maitul). Wild and domesticated Aronia species are found as diploids, triploids, and tetraploids. Genetic improvement of polyploid Aronia genotypes has been limited by suspected apomixis, which may be widespread or distinct to tetraploids. The objectives of this study were to elucidate the reproductive mechanisms of Aronia species and reveal the occurrence of apomixis within the genus and along ploidy lines. Twenty-nine Aronia accessions [five A. melanocarpa (2×), five A. melanocarpa (4×), eight A. prunifolia (3×), four A. prunifolia (4×), six A. arbutifolia (4×), and one A. mitschurinii (4×)] were used in this study. Intra-accession variability was evaluated by growing out progeny from each open-pollinated maternal accession and comparing plant phenotypes, ploidy levels, and amplified fragment length polymorphism (AFLP) marker profiles between the progeny and maternal accession. Progeny of diploid and tetraploid maternal plants had ploidy levels identical to maternal plants, except for UC009 (A. melanocarpa, 2×) which produced a mix of diploids and tetraploids. UC143 and UC149 (A. prunifolia, 3×) produced all triploid offspring, whereas all other triploid accessions produced offspring with variable ploidy levels including 2×, 3×, 4×, and 5×. Pentaploid Aronia has not been previously reported. Diploid accessions produced significant AFLP genetic variation (0.68–0.78 Jaccard’s similarity coefficient) in progeny, which is indicative of sexual reproduction. Seedlings from tetraploid accessions had very little AFLP genetic variation (0.93–0.98 Jaccard’s similarity coefficient) in comparison with their maternal accession. The very limited genetic variation suggests the occurrence of limited diplosporous apomixis with one round of meiotic division in tetraploid progeny. Triploid accessions appear to reproduce sexually or apomictically, or both, depending on the individual. These results support our understanding of Aronia reproductive mechanisms and will help guide future breeding efforts of polyploid Aronia species.